Search results

...n package; instead it is meant to serve as an analytical backend for other data visualization software, mainly GIS.

...no loss of efficiency compared to analysis of a combined dataset including data from all individual studies. * HPC_{{uc:{{#var:app}}}}_EX - example data directory

Genome-wide association analysis of imputed data. ...t for association in samples with differential relationships, facilitating analysis in family-based studies, studies performed in human genetically isolated po

...genotype data as well as summary SNP p-values from a previous GWAS or meta-analysis.

...al features include functionality for mega and meta-genetic analyses where data from diverse cohorts can be pooled to improve statistical significance.

...iling delivers an extended analysis of a DataFrame while allowing the data analysis to be exported in different formats such as html and json.

...ogenetic and population genetic analyses, and small file sizes that enable data sharing and distribution. ...lore.ieee.org/document/7360178 Pease JB and BK Rosenzweig. 2018. "Encoding Data Using Biological Principles: the Multisample Variant Format for Phylogenomi

...s of the fBIRN QA procedures and are also distributed as part of the fBIRN Data Upload Scripts.

...we believe that GUAVA is a powerful and time saving tool for ATAC-seq data analysis. The GUAVA setup contains a script to configure and install dependencies wh

...m, which means you can use only the modules you are interested in for your data. ...ation: MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis. If certain software wrapped into metaWRAP were integral to your investigat

...gory: Geospatial]][[Category:Climate]][[Category:Visualization]][[Category:Data Science]] ...riables may be defined interactively as mathematical expressions involving data set variables. Calculations may be applied over arbitrarily shaped regions.

...icing graph). AltAnalyze is compatible with various data inputs for RNASeq data (FASTQ, BAM, BED), microarray platforms (Gene 1.0, Exon 1.0, junction and 3

...is on called genotypes. This is especially useful for low and medium depth data. The software is written in C++ and has been used on large sample sizes. ...r manipulating '.bam' files, but solely a tool to perform various kinds of analysis. We recommend the excellent program SAMtools for outputting and modifying b

TASSEL stands for Trait Analysis by aSSociation, Evolution and Linkage. Its primary function continues to be ...rincipal component analysis, cluster analysis, missing data imputation and data visualization.  TASSEL development has been led by a group focused on maiz

...o this list. Discussion about any aspects of biological computing and data analysis is also welcome.

In order to complete the DNA methylation data analysis more conveniently, for DNA methylation analysis. During the execution of BatMeth2 Tool, an

[[Category:Software]][[Category:Performance Analysis]] ...able fast and interactive rendering of very complex performance monitoring data.

[[Category:Software]][[Category:Data Science]] ...al parallel processing framework, PROOF, that can considerably speed up an analysis.

...he alignment data. The quantified events can then be used for differential analysis.

S.A.G.E. (Statistical Analysis for Genetic Epidemiology) ...rograms for use in the genetic analysis of family, pedigree and individual data.

...nient handling and visualization of single-cell data to enable exploratory analysis.

ClonalFrame can be applied to any kind of sequence data, from a fragment of DNA to whole genomes. It is well suited for the analysis of MLST

...cient solution for analysis of large scale base-resolution DNA methylation data, bisulfite sequencing or single molecule direct sequencing. ...le and differential methylation for multiple samples, and other downstream analysis.

...ary preparation. Such nucleotides can potentially case hurdles during data analysis and hereby need to be removed. In additional, the noise, which is presented

...C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. It should be used for resea RW Cox. AFNI: Software for analysis and visualization of functional magnetic resonance neuroimages. Computers a

Analysis of alternative polyadenylation (APA) from RNA-seq data (human and mouse). QAPA consists of two main components: ...od for the systematic analysis of alternative polyadenylation from RNA-seq data. Genome Biol. 19, 45.]

...egory:Software]][[Category:Utility]][[Category:GPU]][[Category:Performance Analysis]] ...based analysis scripts for post-processing results. The rules-based guided analysis helps isolate and fix memory throughput, compute, and occupancy inefficienc

...omprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. ..., C. Beckmann, M. Jenkinson, S.M. Smith. Bayesian analysis of neuroimaging data in FSL. NeuroImage, 45:S173-86, 2009

...c analysis, it can also be used to deal with clustering trees or any other data that can be represented as a hierarchical tree. ...v.msw046 ETE 3: Reconstruction, analysis and visualization of phylogenomic data. Jaime Huerta-Cepas, Francois Serra and Peer Bork. Mol Biol Evol 2016; doi:

...ded statistical processes used to test hypotheses about functional imaging data. These ideas have been instantiated in software that is called SPM. ...time-series from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT, EEG and MEG.

...for performing meta-analyses, and derivative analyses using meta-analytic data, of the neuroimaging literature. While meta-analytic packages exist which i ...ng (MACM) analysis, peaks2maps image reconstruction, and contrast map meta-analysis. '''Each workflow should generate a boilerplate paragraph with details abou

TrackVis is a software tool that can visualize and analyze fiber track data from diffusion MR imaging (DTI/DSI/HARDI/Q-Ball) tractography. Features of ...ormat of the track data file allowing users to integrate customized scalar data into the track file and visualize and analyze it. Save and restore scenes i

Methylpy, a pyhton-based analysis pipeline for (single-cell) (whole-genome) bisulfite sequencing data

...effects modelling tool used in population pharmacokinetic/pharmacodynamic analysis. ...in previous versions. NONMEM® can be used to simulate data as well as fit data.

* automate simulation post-processing, visualization, and data analysis tasks, * integrate OVITO’s file I/O, data analysis, and rendering capabilities into custom workflows and external Python progr

...e core distribution provides a basic set of features for data integration, analysis, and visualization.

...y or functional annotations (primarily from ENCODE and Roadmap epigenomics data) to find features relevant to a phenotype of interest. ...0K Consortium, Ian Dunham, Ewan Birney and Nicole Soranzo. GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction. doi:

...Nalyzer) is a comprehensive toolbox for interactively analyzing microbiome data. All the interactive tools * Taxonomic analysis using the NCBI taxonomy or a customized taxonomy such as SILVA

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a co ...(e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for

...tics bottleneck in preparing and utilising such data for phylogenetic data analysis. We present, MitoPhAST, an automated tool that: ...ncorporates nuclear gene sequences (if supplied by user) into phylogenetic analysis.

...orming both cis- and trans-eQTL analysis given a set of raw genetic marker data and expression values.

...from representative sequences of OTUs, and through downstream statistical analysis, visualization, and production of publication-quality graphics. QIIME has b

event-related EEG, MEG and other electrophysiological data using independent component analysis (ICA), time/frequency analysis, and other methods

prior to phylogenetic analysis. Gblocks selects blocks in a similar way as the final alignment more suitable for phylogenetic analysis. Gblocks outputs

...and data visualization through clustering analysis and gene-set enrichment analysis. RNAlysis: analyze your RNA sequencing data without writing a single line of code. BMC Biology, 21, 74.

...two data models for handling gridded and station data. GrADS supports many data file formats, including binary (stream or sequential), GRIB2, NetCDF, and H

...provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition

...integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercia

...astA format). FAST tools expose the power of Perl and BioPerl for sequence analysis to non-programmers in an easy-to-learn command-line paradigm. .../articles/10.3389/fgene.2015.00172/full Lawrence et al. (2015). FAST: FAST Analysis of Sequences Toolbox in Frontiers in Genetics, and Stajich et al. (2002)]

Pomoxis started life as a set of services to perform analysis of squiggles as draft assemblies. Many of these tools are used by the research data analysis

...cks provenance, and provides lightweight tools for building out customized analysis pipelines. * A 'catalog' database for pairing metadata with and organizing NGS data files.

uses high-throughput genome sequencing data as an input and performs graph-based clustering analysis of sequence read similarities to identify

...mprehensive analysis framework for T-cell and B-cell repertoire sequencing data. ...le?id=10.1371/journal.pcbi.1004503 Shugay M et al. VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires. PLoS Comp Biol 2015; 11(11):e1004503-e10045

...es. The corresponding parameters (except for GTR) can be inferred from the data set. ...n, and A. von Haeseler (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics. 18:502-504.]

...erential analysis, and feature linkage between peaks and genes that aid in data interpretation.

...urce project to provide tools for downstream analysis of Complete Genomics data. The focus is to provide command line utilities, but a C++ API is available

...is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationship ...fographics and illustrations with a high data-to-ink ratio, richly layered data and pleasant symmetries. You have fine control each element in the figure t

...ete analysis of bacterial genomes. The goal of Bactopia is to process your data with a broad set of tools, so that you can get to the fun part of analyses Petit III RA, Read TD, Bactopia: a flexible pipeline for complete analysis of bacterial genomes. mSystems. 5 (2020), https://doi.org/10.1128/mSystems.

...Rare Variant tests, is a flexible software package for genetic association analysis for sequence datasets. ...nd Comprehensive Tool for Rare Variant Association Analysis Using Sequence Data. Bioinformatics 2016 32: 1423-1426.]

...downstream Biopieces until the data stream is terminated at the end of the analysis as outlined below: * BP_DATA - biopieces data directory

...is a state of the art software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of sample *phase genotype data (i.e. infer haplotypes) for unrelated individuals, parent-offspring pairs,

...olecular QTL discovery and analysis. It allows to go from the raw sequence data to collection of molecular Quantitative Trait Loci (QTLs) in few easy-to-pe ...068635 Delaneau et al. A complete tool set for molecular QTL discovery and analysis.]

..., in our turn, will provide the hardware and software support for the data analysis pipeline they create for you. ...T databases, which serve both Galaxy and the command line blast see <code>/data/reference/blast/db</code>.

HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays. ...ntation chapter A tour through HTSeq] first for an overview on the kind of analysis you can do with HTSeq and the design of the package, and then look at the r

...ltiplexing. This new tool provides a better end-to-end user experience for analysis of multiplexed samples.

...ecognized to facilitate reasoning. This is a software for Exploratory Data Analysis, a paradigm appeared in the Visual Analytics field of research.

...ds, generate gene-cell matrices and perform clustering and gene expression analysis. Cell Ranger 1.2 supports libraries generated by the Chromium Single Cell 3 * HPC_{{uc:{{#var:app}}}}_REF - reference data directory

This repository contains instructions for processing and repeat analysis of sequence data generated with the PacBio No-Amp Targeted Sequencing

...meters or statistics for specific regions, and thus perform sliding window analysis over large genomic regions. ...t/28/2/298.full Lischer HEL and Excoffier L (2012) PGDSpider: An automated data conversion tool for connecting population genetics and genomics programs. B

...d-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts. *rnaseq - Evaluate RNA-seq alignment data

...ed on local computers or on HPC environments to manage analysis of RNA-Seq data. Users can use the easy-to-use APIs to popular bioinformatic tools provided

...tions via meta-analysis, without direct exchange of genotype and phenotype data. ...11-288 Magi R, Morris AP: GWAMA: software for genome-wide association meta-analysis. BMC Bioinformatics 2010, 11:288.]

...th neurological and psychiatric diseases and the acquisition of multimodal data (neuroimaging, clinical and cognitive evaluations, genetics...), most often ...x, PETPVC, SPM), machine learning (Scikit-learn) and the BIDS standard for data organization.

...free software tools to facilitate the analysis of high-throughput genomics data sets. The package is currently a work-in-progress and infrequently updated. .../S0002-9297(07)63775-6 Wang K, Li M, Bucan M. Pathway-based approaches for analysis of genome-wide association studies. American Journal of Human Genetics, 81:

...bForAlphaImpute (Kerr and Kinghorn, 1996). All information on the model of analysis, input files and their layout, is specified in a single parameter file.

...llites conforming to user specified parameters. Each of the three separate analysis modules also can be used independently to provide greater flexibility or to ...ughput DNA sequence data (ver. 1.1, February 2014): U.S. Geological Survey Data Series 778.

[[Category:Software]][[Category:Performance Analysis]][[Category:Performance Analysis]] * CPU Power and Temperature data

LIQA (Long-read Isoform Quantification and Analysis) is an Expectation-Maximization alternative splicing (DAS) events using long-read RNA-seq data. LIQA incorporates

[[Category:Data Science]] ...-code interface offers an easy introduction for beginners, and an advanced data science set of tools for experienced users.

...from representative sequences of OTUs, and through downstream statistical analysis, visualization, and production of publication-quality graphics. QIIME has b

...nstructing a taxonomic tree of the results, and for performing comparative analysis of the taxonomic profiles for multiple metagenomic datasets.

...applicable and hopefully useful beyond PAFTOL, e.g. for processing HybSeq data in general. Functionality can be accessed either via the paftools script or

...languages for the analysis of recombination rates from population genetic data. The package is available either as C/C++ source code. *convert: Simple manipulation of DNA sequence data

Molecular Evolutionary Genetics Analysis Software suite for analyzing DNA and protein sequence data from species and populations.

De novo assembly of RNAseq data using ABySS ....html Robertson, G., et al. 2010. De novo assembly and analysis of RNA-seq data. Nature Methods 7, 909-912(2010)]

Biodiverse is a tool for the spatial analysis of diversity using indices based on taxonomic, phylogenetic, trait and matr ...W., Lubarsky, E. & Rosauer, D.F. (2010) Biodiverse, a tool for the spatial analysis of biological and related diversity. Ecography. Vol 33, 643-647 (Version 1.

...es in SNV, ASM and DMR. Command-line Toolset for Bisulfite Sequencing Data Analysis

.... The core of the Parabricks software is its data pipeline which takes raw data and transforms it according to the user's requirements. # Set data directories

|{{#vardefine:url|https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool}} ...Atlas (TCGA) reach sizes of 200-300 GB. In such cases, a high performance data download and submission client is essential.

|{{#vardefine:url|https://github.com/neherlab/pan-genome-analysis}} ...notated bacterial strains as input (e.g. NCBI RefSeq records or user's own data in GenBank format). Alls genes from all strains are compared to each other

...tering of the data. It support NGS data (such as Illumina), 3rd generation data (Pacbio/Nanopore) and assembled sequences (FASTA).

...nd data mining. It provides simple and efficient tools for predictive data analysis. scikit-learn is built on NumPy, SciPy, and matplotlib, and is open source

...much of the genome supports each relationship, using Bayesian concordance analysis. BUCKy does not assume that genes (or loci) all have the same topology. Ins ...CKy: Gene tree / species tree reconciliation with the Bayesian concordance analysis. Bioinformatics (advance access).]

...ally dimorphic characteristics. Special attention needs to be given to the analysis of X due to its unique inheritance pattern and X-inactivation. These analyt ...ddanda A, Ma L, Guo Y, Zhou Z, Keinan A. "XWAS: a toolset for genetic data analysis and association studies of the X chromosome." Journal of Heredity. 2015;106

* HPC_{{uc:{{#var:app}}}}_EXE - test data directory * HPC_{{uc:{{#var:app}}}}_TAX- taxonomy data directory

...earch analyses you need to [[Transfer_Data|upload]] and [[Storage|manage]] data. Note that misuse of the storage systems is the second main reason for acco ===Transferring Data===

FAN-C provides a pipeline for analysing Hi-C data starting at mapped paired-end sequencing reads. ...work for the analysis and visualisation of chromosome conformation capture data. ''Genome Biol'' 21, 303. https://doi.org/10.1186/s13059-020-02215-9

...el improves on the original Strelka method for liquid and late-stage tumor analysis by accounting for possible tumor cell contamination in the normal sample. A

Creates genomic builds, calls SNPs, detects indels, and counts reads from data generated from one or more sequencing runs. ...can create genomic builds, call SNPs, detects indels, and count reads from data generated from one or more runs of the Genome Analyzer across a broad range

...be used to process any NGS amplicon data and includes databases setup for analysis of fungal ITS, fungal LSU, bacterial 16S, and insect COI amplicons.

...oftware tool for automated, robust, scalable and reproducible SLAMseq data analysis. Diagnostic plotting features and our MultiQC plugin will make your SLAMseq data ready for immediate QA and interpretation.

...and quantitative analysis of in-vivo magnetic resonance spectroscopy (MRS) data. ...Processing, Reconstruction & Estimation of Magnetic Resonance Spectroscopy Data. J Neurosci Meth 343:108827 (2020).]

iMOKA is a software that enables a comprehensive analysis of sequencing data indexing, iMOKA can easily integrate data from multiple experiments and also

...ing centers. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard ...Manke T. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Research. 2016 Apr 13:gkw257.]

...DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. ...ng findMotifsGenome.pl to store the pre-parsed genome files locally as the data/genomes/*/preparsed/ are not writable by users.

...ion before further downstream analysis. Currently, it works only for human data.

expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data. It is based on

...the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety. ...tomated method for constructing SNP matrices from next-generation sequence data. PeerJ Computer Science 1:e20 https://doi.org/10.7717/peerj-cs.20]

Scalable LC-MS Analysis Workflow slaw /data/apps/tests/slaw/test_input /data/apps/tests/slaw/test_output

...he main application of SortMeRNA is filtering rRNA from metatranscriptomic data. ...MeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data", Bioinformatics (2012), doi: 10.1093/bioinformatics/bts611.]

[[Category:Software]][[Category:Data Science]] ...s to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaV

...a science tools that can be used to interrogate even biobank-scale genomic data (e.g. UK Biobank, gnomAD, TopMed, FinnGen, and Biobank Japan).

...resources for running jobs, transparent user account access and convenient data upload, as well as full system and user support by the RC staff. ...l.edu UFRC Support Ticket System] to request adding new tools or reference data to the Galaxy and to file problem reports. '''Note: If you are submitting a

...pe is a workflow designed for analysis of next generation sequencing (NGS) data from viral pathogens. It produces a number of results in a curated format. ...line for assessing viral genetic diversity from high-throughput sequencing data." Bioinformatics, January. doi:10.1093/bioinformatics/btab015.

[[Category:Transfer Data]] ...een two computer systems. UFRC now provides a URL for users to rsync their data to and from the cluster. The basic syntax of the rsync command is:

...greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools.

...VisIt is capabable of visualizing data from over 120 different scientific data formats.

...ndors (Agilent, Bruker, LECO, Sciex, Shimadzu, Thermo, and Waters). Common data formats such as netCDF (AIA) and mzML, can also be managed in our project. * spectral deconvolution for both GC/MS and data-independent MS/MS,

Summary-data-based Mendelian Randomization ...Zhu et al. 2016 Nature Genetics). The methodology can be interpreted as an analysis to test if the effect size of a SNP on the phenotype is mediated by gene ex

...': Matlab provides rich libraries of image processing techniques for image analysis. ...AI to the task at hand by continuously learning from user interactions and data.

A novel algorithm for BSA-Seq data analysis

...at makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical ...roblems (like SNP calling) as well as enabling exploratory research on NGS data.

...implements a novel algorithm ("Mosaic Matching") for large-scale sequence analysis and is now available in terms of an open source C library. UProC is up to t

...ON is technology-agnostic in that it works from mapped SAM files, allowing data from different sequencing platforms (i.e. PacBio and Oxford Nanopore) to be A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification. Dana Wyman, Gabrie

Anvio is an analysis and visualization platform for ‘omics data.

...s a highly sensitive program in detecting differential sites from ChIP-seq data. ...iffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates. PLoS ONE 8(6): e65598. [http://www.plosone.org/

...at the Genome Institute at Washington University to detect variants in NGS data.

...e toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studie

...loo-chee) is a software package that was initially developed for analyzing data collected from ultraconserved elements in organismal genomes. * The assembly of raw read data to contigs

prediction and analysis. It includes algorithms for secondary structure can take a number of different types of experiment mapping data to

..., and profiling functionality of a comprehensive development tool with the data exploration, interactive execution, deep inspection, and beautiful visualiz

...e for identifying and structural variants (SVs) from paired-end sequencing data.

...e for analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data.

...ics software suite for analyzing single molecule, real-time DNA sequencing data.

...rence of false positives. PosiGene was tested on simulated as well as real data to ensure the reliability of the predicted positively selected genes.

...calculation, gene expression quantification, differential gene expression analysis as well as visualization. In order to set up and perform analyses quickly R

...OG/GO Pathways databases). All functional annotation data derived from the analysis of transcripts is integrated into a SQLite database which allows fast effic

...uencies as prior information for the unobserved genotypes in low-depth NGS data.

...reads to both genes & transposable elements. It then performs differential analysis using DESeq.

PIPE-CLIP: a comprehensive tool for CLIP-seq data analysis

...and-line tools dedicated to the processing and analysis of spinal cord MRI data.

...ation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also it ...visualization and analysis of high-throughput sequence-based experimental data.

Pipeline developed by Mission Bio for the analysis of single-cell sequencing data in the form of raw reads (fastq) from Illumina sequencing technology paired

Denovo Genome Analysis Pipeline for Prokaryotic Species * HPC_{{uc:{{#var:app}}}}_EXE - example data directory

...(SNVs) and short indels (up to 30 bp) in next-generation sequencing (NGS) data. By integrating and filtering the output of eight individual variant callin $ appreci8 /path/to/your/data/

...mics Using Generative AI. A Python package for single-cell multi-omic data analysis using pretrained foundation models.

...fast quality control and preprocessing of high throughput sequencing (HTS) data. It consists of three modules: filter, filtersRNA and filterMeta.

...plement the most commonly used clustering methods for gene expression data analysis. The clustering methods can be used in several ways. Cluster 3.0 provides a

...ms and library functions for the manipulation and analysis of astronomical data. All the programs share the same basic command-line user interface for the

...and accurate analysis of raw T- or B- cell receptor repertoire sequencing data. ...& Dmitriy M. Chudakov. "Antigen receptor repertoire profiling from RNA-seq data." Nature Biotechnology 35, 908–911 (2017)

STUMPY is a powerful and scalable Python library for modern time series analysis. variety of data mining tasks such as:

...RiverGIS serves as a data pre-processing and analysis tool for geographic data.RiverGIS, as its name implies, is geographical information system (GIS) sof ...work on other flavors of UNIX). RiverGIS is configured to store all loaded data in memory, thus processing speed will be influenced by file size.

[[Category:Software]][[Category:Statistics]][[Category:Data Science]] ...erence for the functions and procedures you may need to do the statistical analysis using SAS.

...h-quality results in a reproducible way directly integrated into your data analysis workflows.

...es as accurately as achieved by careful manual analysis of electrophoresis data, the prior highest-accuracy standard. ShapeMapper 2 can be used to read out * HPC_{{uc:{{#var:app}}}}_EXE - test data directory

...n programs used to perform rapid time delay analysis on functional imaging data to find time lagged correlations between the voxelwise time series and othe

AEGeAn: analysis and evaluation of genome annotations ...into a single library that includes executable programs as well as several data structures and modules callable via a C API.

statistical analysis of graphs. It contains several general graph measurements, data structures and algorithms, such as vertex and edge

...long-read (ONT or PacBio) or short-read (Illumina) whole genome sequencing data of DNA extracted from wastewater. It was developed for SARS-CoV2 and its va

...lows you to draw regions of interest which can aid lesion mapping and fMRI analysis. It provides sophisticated rendering.

...rify whole chloroplast genome sequences. For most datasets with sufficient data, Fast-Plast is able to produce a full-length de novo chloroplast genome ass Currently, Fast-Plast is written to accomodate Illumina data, although most data types could be used.

[[Category:Data Science]] ...PDFs, etc—so-called “dark data”—that would be valuable for further textual analysis and visualization. While several packages exist for extracting content from

...ted models to genome-wide association studies (GWAS) and other large-scale data sets. ...Xiang Zhou and Matthew Stephens (2012). Genome-wide efficient mixed-model analysis for association studies. Nature Genetics 44, 821–824.]

...sive analysis pipeline for circRNA detection and quantification in RNA-Seq data

RiboTaper is a new analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the ...: Detecting actively translated open reading frames in ribosome profiling data Nature methods]

...mation System (GIS) software suite used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visu ...es. Solar energy R&D in the European Community, series F – Solar radiation data, Dordrecht (D. Reidel), 3, 71, 81-83.

...Magnetic Resonance Imaging (fcMRI). CONN is used to analyze resting state data (rsfMRI) as well as task-related designs.

and analysis of molecular structures and related data, including density

...data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application. A composable workflow of existing tools and algorithms, combin

...le on Amazon Cloud (EC2) to utilize on-demand computing resources for data analysis.

...tation site or CTK analysis is a computational method to analyze HITS-CLIP data for determining the exact protein-RNA crosslink sites and thereby mapping p

...is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images. Space Ranger allows us

--data-file=DATA_FILE Specify a data file for LoadData modules that use the

...r the fitting and quantification of proton magnetic resonance spectroscopy data. FSL-MRS handles both single voxel and multi-voxel (MRSI) datasets. FSL-MRS Clarke WT, Stagg CJ, Jbabdi S. FSL-MRS: An end-to-end spectroscopy analysis package. Magnetic Resonance in Medicine 2021;85:2950–2964 doi: 10.1002/mr

...algorithms and colormaps. It provides for easy communication with external analysis tasks and is highly configurable and extensible via XPA and SAMP.

Crosslinking induced mutation site or CIMS analysis is a computational method to analyze HITS-CLIP data for determining the exact protein-RNA

...ent of Physiology. It is part of MountainLab, a general framework for data analysis and visualization.

...udies comprising a large number of samples, and for applications where the analysis delivery time is a critical factor, such as pathogen identification from cl

...computations are bread and butter for NGS analysis but the high volume of data make them execute very slowly or even failing to compute.

...r genotype calling, and are particularly suitable for low sequencing depth data. ...: methods for population genetics analyses from next-generation sequencing data.Fumagalli M, Vieira FG, Linderoth T, Nielsen R. Bioinformatics. 2014 May 15

...ts .dcc files, which can then be uploaded to the GeoMx DSP system for data analysis.

...benchmark a variety of method or tools for next-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation di

...the SV with know breakpoints on the contig. These data feed into powerful analysis tools that use the reference and the contigs, such as the SMRT-SV genotyper

...The manual provides information about the models, about how to format the data file, how to specify the user-defined parameters, and how to interpret the ...1 Gautier M. Genome-Wide Scan for Adaptive Differentiation and Association Analysis with population-specific covariables. Genetics, 201: 1555-1579.]

...ther molecular functions from metagenomic or metatranscriptomic sequencing data.

ClonalFrameML can be applied to any type of aligned sequence data, but is especially aimed at analysis of whole genome sequences. It is able to

...r these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers

* HPC_{{uc:{{#var:app}}}}_DAT - data directory ...JC, Paterson AH. (2012) MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res, 40(7): e49.]

...ys leading-edge algorithms for registering and segmenting multidimensional data.

|{{#vardefine:url|https://nanoporetech.com/nanopore-sequencing-data-analysis}} Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies' basecall

...stom or haplotype-specific sequences. The latter allows haplotype-specific analysis, which is useful in studies of allelic imbalance. The posterior distributio

...eural network to call genetic variants from next-generation DNA sequencing data.

...oint genotyping of structural variants (SVs) using whole genome sequencing data. Users must supply a VCF file of sites to genotype (which may be generated ...G T Marth, A R Quinlan, and I M Hall. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Meth 12, 966–968 (2015). doi:10.1038/nmeth.3505.

...g, visualization and analysis of mass spectrometry based molecular profile data. It is based on the original MZmine toolbox described in 2006 Bioinformatic

...The method is accurate, simple and fast to execute and, for transcriptome data, requires low depth of coverage. Known HLA class I/class II reference seque ...ce contigs equal or larger than 200nt in length are considered for further analysis, as longer contigs better resolve HLA allelic variants. Reciprocal BLASTN a

...l platform for the analysis and manipulation of high-throughput sequencing data such as RNA-seq and ChIP-seq. GenomicTools implements a variety of mathemat

SHEsisPlus is a a software package for analysis of genetic association, Hardy-weinberg equilibrium, linkage disequilibrium ...h U, Gebhardt C, Selbig J, Kersten B.Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT. BMC Genomics 2008 Jul 30;9:356. do

: Crusoe et al., The khmer software package: enabling efficient sequence analysis. 2014. doi: 10.6084/m9.figshare.979190 ...rence-Free Algorithm for Computational Normalization of Shotgun Sequencing Data

...y be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide v

If you use pyGenomeTracks in your analysis, you can cite the following papers: ...ez F, Manke T. pyGenomeTracks: reproducible plots for multivariate genomic data sets. Bioinformatics. 2020 Aug 3:btaa692. doi: 10.1093/bioinformatics/btaa6

...ical software package that provides everything you need for data analysis, data management, and graphics.

...sagree'''. Each option of this software is also complemented with a random analysis to test the null hypothesis that any comparison is not better than random. ...rams/topd software website]. For your convenience and testing, all example data and output are provided in the installation directory.

...emble discreet 'targets' contained within next-generation shotgun sequence data. ARC decomplexifies the traditionally difficult problem of assembly by subs

...prediction process (e.g. DCC and CircTest), publicly available downstream analysis tools are rare.

...profile''' extracts marker gene sequences from your own Fungal biological data, including genome sequences, transcriptome sequences, and proteome sequence ...e of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi. Nucleic Acids Research, 51(D1), D777-D784, doi:10.1093/nar/gkac89

...om this SAMStat can be used to verify individual processing steps in large analysis pipelines. ...nn et al. (2010) "SAMStat: monitoring biases in next generation sequencing data." Bioinformatics doi:10.1093/bioinformatics/btq614 [PMID: 21088025]

...n of gene or isoform abundance is a fundamental step in many transcriptome analysis tasks, such as determining differential expression between biological sampl ...experiments. In the paper, we demonstrate that, on both real and synthetic data, Sailfish is as accurate as existing read mapping-based tools such as eXpre

...ns to the x86 instruction set that accelerate single-instruction, multiple-data (SIMD) computations - often referred to as vectorization. For each of the f ...this is likely a good thing in terms of finding the ML tree and a thorough analysis, users should understand that this stage will not see a reduction in run ti

[[Category:Biology]][[Category:Data]] All databases are full mirrors of NCBI data

:*Cancer variants analysis ...a new reference database unless you need a custom database built from your data. Please provide a fasta file and an annotation file for building the custom

USEARCH is a unique high-throughput sequence analysis tool. It is a distributed as single binary program that implements a suite abstract ={Motivation: Biological sequence data is accumulating rapidly, motivating the development of improved high-throug

[[Category:Data]][[Category:Essentials]] ...t rule of using the home directory is to not use it for reading or writing data files in any analyses run on HiPerGator. It is permissible to keep software

MATLAB is a programming environment for algorithm development, data analysis, visualization, and numerical computation. Using MATLAB, you can solve tech ...mmunications, control design, test and measurement, financial modeling and analysis, and computational biology. MATLAB is the language of technical computing f

...the Message Passing Interface (MPI). This means, that if you conduct your analysis on a computing cluster composed of several machines (a.k.a. nodes), the mem

#* Blue (<code>/blue</code>): High-performance storage for most data during analyses * Generally speaking, interactive work other than managing jobs and data is ''discouraged'' on the login nodes.