Search results

• CASAVA
  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
  3 KB (340 words) - 18:23, 12 August 2022
• AMPtk
  ...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.
  2 KB (289 words) - 12:41, 12 August 2022
• Slamdunk
  ...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.
  3 KB (294 words) - 20:55, 27 May 2022
• Osprey
  ...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).]
  2 KB (280 words) - 18:01, 19 August 2022
• Imoka
  iMOKA is a software that enables a comprehensive analysis of sequencing data indexing, iMOKA can easily integrate data from multiple experiments and also
  3 KB (346 words) - 17:07, 27 May 2022
• DeepTools
  ...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.]
  3 KB (360 words) - 14:35, 15 August 2022
• HOMER
  ...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.
  3 KB (330 words) - 18:19, 15 August 2022
• Ngscheckmate
  ...ion before further downstream analysis. Currently, it works only for human data.
  3 KB (390 words) - 18:12, 27 May 2022
• EXpress
  expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data. It is based on
  3 KB (383 words) - 18:53, 12 August 2022
• NLP
  [[Category:Software]][[Category:Machine Learning]][[Category:Data Science]][[Category:Help]] ...iomedical NLP tasks, featuring advanced models for tasks like medical text analysis, drug interaction extraction, and patient information processing. It also a
  8 KB (1,126 words) - 19:55, 14 May 2024
• SNP-Pipeline
  ...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]
  3 KB (306 words) - 17:00, 10 June 2022
• SLAW
  Scalable LC-MS Analysis Workflow slaw /data/apps/tests/slaw/test_input /data/apps/tests/slaw/test_output
  3 KB (389 words) - 23:49, 21 August 2022
• SortMeRNA
  ...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.]
  3 KB (299 words) - 17:00, 10 June 2022
• ParaView
  [[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
  3 KB (416 words) - 21:28, 13 October 2023
• Hail
  ...a science tools that can be used to interrogate even biobank-scale genomic data (e.g. UK Biobank, gnomAD, TopMed, FinnGen, and Biobank Japan).
  3 KB (353 words) - 17:42, 19 October 2021
• Galaxy
  ...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
  4 KB (562 words) - 18:05, 9 November 2022
• V-pipe
  ...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.
  3 KB (296 words) - 17:20, 22 August 2022
• Rsync
  [[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:
  3 KB (506 words) - 21:25, 28 July 2023
• Popoolation
  ...greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools.
  3 KB (321 words) - 21:23, 6 December 2019
• Visit
  ...VisIt is capabable of visualizing data from over 120 different scientific data formats.
  3 KB (403 words) - 14:47, 15 March 2024
• Ms-dial
  ...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,
  3 KB (385 words) - 13:32, 19 August 2022
• SMR
  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
  3 KB (362 words) - 18:27, 19 August 2021
• Computer Vision
  ...': 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.
  4 KB (563 words) - 20:59, 21 December 2022
• PyBSASeq
  A novel algorithm for BSA-Seq data analysis
  2 KB (235 words) - 17:14, 1 June 2022
• GATK
  ...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.
  4 KB (540 words) - 16:53, 15 August 2022
• Uproc
  ...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
  3 KB (418 words) - 20:53, 12 August 2022
• Talon
  ...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
  3 KB (321 words) - 15:13, 23 September 2022
• Anvio
  Anvio is an analysis and visualization platform for ‘omics data.
  2 KB (237 words) - 14:20, 12 August 2022
• DiffReps
  ...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/
  4 KB (474 words) - 14:41, 15 August 2022
• VarScan
  ...at the Genome Institute at Washington University to detect variants in NGS data.
  3 KB (324 words) - 20:54, 12 August 2022
• Ipyrad
  ...e toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studie
  2 KB (239 words) - 19:00, 15 August 2022
• Phyluce
  ...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
  4 KB (517 words) - 18:23, 21 August 2022
• RNAstructure
  prediction and analysis. It includes algorithms for secondary structure can take a number of different types of experiment mapping data to
  3 KB (359 words) - 21:58, 21 August 2022
• Spyder
  ..., and profiling functionality of a comprehensive development tool with the data exploration, interactive execution, deep inspection, and beautiful visualiz
  3 KB (350 words) - 18:56, 21 August 2022
• Hyb
  ...e for analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data.
  2 KB (247 words) - 15:07, 10 June 2022
• GASVPro
  ...e for identifying and structural variants (SVs) from paired-end sequencing data.
  2 KB (248 words) - 18:57, 12 August 2022
• PacBio
  ...ics software suite for analyzing single molecule, real-time DNA sequencing data.
  2 KB (250 words) - 20:10, 24 August 2022
• PosiGene
  ...rence of false positives. PosiGene was tested on simulated as well as real data to ensure the reliability of the predicted positively selected genes.
  3 KB (358 words) - 21:22, 6 December 2019
• READemption
  ...calculation, gene expression quantification, differential gene expression analysis as well as visualization. In order to set up and perform analyses quickly R
  3 KB (352 words) - 17:58, 1 June 2022
• Trinotate
  ...OG/GO Pathways databases). All functional annotation data derived from the analysis of transcripts is integrated into a SQLite database which allows fast effic
  3 KB (344 words) - 20:29, 7 December 2023
• Pcangsd
  ...uencies as prior information for the unobserved genotypes in low-depth NGS data.
  3 KB (343 words) - 18:21, 8 December 2023
• TEToolkit
  ...reads to both genes & transposable elements. It then performs differential analysis using DESeq.
  2 KB (259 words) - 20:46, 12 August 2022
• Pipe-clip
  PIPE-CLIP: a comprehensive tool for CLIP-seq data analysis
  2 KB (254 words) - 21:22, 6 December 2019
• SpinalCordToolbox
  ...and-line tools dedicated to the processing and analysis of spinal cord MRI data.
  2 KB (253 words) - 18:43, 1 June 2022
• Artemis
  ...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.
  3 KB (378 words) - 14:53, 12 August 2022
• Tapestri
  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
  2 KB (258 words) - 19:07, 1 June 2022
• DeNoGAP
  Denovo Genome Analysis Pipeline for Prokaryotic Species * HPC_{{uc:{{#var:app}}}}_EXE - example data directory
  2 KB (272 words) - 21:20, 6 December 2019
• Appreci8
  ...(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/
  4 KB (561 words) - 14:25, 12 August 2022
• ScGPT
  ...mics Using Generative AI. A Python package for single-cell multi-omic data analysis using pretrained foundation models.
  2 KB (258 words) - 16:01, 7 August 2023
• SOAPnuke
  ...fast quality control and preprocessing of high throughput sequencing (HTS) data. It consists of three modules: filter, filtersRNA and filterMeta.
  2 KB (264 words) - 14:12, 6 April 2020
• Cluster3
  ...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
  2 KB (274 words) - 18:37, 12 August 2022
• Gnuastro
  ...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
  2 KB (270 words) - 19:16, 8 January 2024
• MiXCR
  ...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)
  3 KB (340 words) - 21:22, 6 December 2019
• Stumpy
  STUMPY is a powerful and scalable Python library for modern time series analysis. variety of data mining tasks such as:
  3 KB (430 words) - 15:16, 13 April 2023
• RGIS
  ...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.
  3 KB (370 words) - 20:27, 24 August 2022
• SAS
  [[Category:Software]][[Category:Statistics]][[Category:Data Science]] ...erence for the functions and procedures you may need to do the statistical analysis using SAS.
  5 KB (775 words) - 13:48, 15 September 2023
• Blast2GO CLI
  ...h-quality results in a reproducible way directly integrated into your data analysis workflows.
  2 KB (282 words) - 20:19, 24 August 2022
• ShapeMapper
  ...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
  3 KB (387 words) - 21:24, 6 December 2019
• Rapidtide
  ...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
  2 KB (281 words) - 13:58, 7 May 2020
• AEGeAn
  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.
  2 KB (287 words) - 16:31, 10 June 2022
• Graph-tool
  statistical analysis of graphs. It contains several general graph measurements, data structures and algorithms, such as vertex and edge
  2 KB (285 words) - 17:20, 15 August 2022
• C-wap
  ...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
  2 KB (281 words) - 13:16, 15 August 2022
• MRIcroGL
  ...lows you to draw regions of interest which can aid lesion mapping and fMRI analysis. It provides sophisticated rendering.
  2 KB (294 words) - 20:33, 24 August 2022
• Fast-Plast
  ...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.
  4 KB (487 words) - 21:20, 6 December 2019
• Textract
  [[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
  3 KB (304 words) - 13:55, 21 October 2022
• GEMMA
  ...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.]
  2 KB (279 words) - 21:21, 6 December 2019
• Ciriquant
  ...sive analysis pipeline for circRNA detection and quantification in RNA-Seq data
  2 KB (275 words) - 15:00, 30 March 2022
• RiboTaper
  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]
  3 KB (293 words) - 13:48, 20 May 2020
• GRASS
  ...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.
  5 KB (593 words) - 21:27, 14 December 2022
• CONN
  ...Magnetic Resonance Imaging (fcMRI). CONN is used to analyze resting state data (rsfMRI) as well as task-related designs.
  3 KB (293 words) - 20:32, 24 August 2022
• Chimera
  and analysis of molecular structures and related data, including density
  3 KB (296 words) - 18:27, 12 August 2022
• IsoSeq3
  ...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
  3 KB (295 words) - 20:10, 24 August 2022
• MGEScan
  ...le on Amazon Cloud (EC2) to utilize on-demand computing resources for data analysis.
  2 KB (299 words) - 16:58, 10 June 2022
• Ctk
  ...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
  3 KB (297 words) - 16:53, 10 October 2022
• SpaceRanger
  ...is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images. Space Ranger allows us
  3 KB (305 words) - 18:57, 20 October 2021
• CellProfiler
  --data-file=DATA_FILE Specify a data file for LoadData modules that use the
  8 KB (910 words) - 21:29, 21 December 2022
• Fslmrs
  ...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
  3 KB (293 words) - 16:50, 15 August 2022
• DS9
  ...algorithms and colormaps. It provides for easy communication with external analysis tasks and is highly configurable and extensible via XPA and SAMP.
  3 KB (322 words) - 13:07, 6 June 2022
• CIMS
  Crosslinking induced mutation site or CIMS analysis is a computational method to analyze HITS-CLIP data for determining the exact protein-RNA
  3 KB (315 words) - 17:21, 10 June 2022
• MountainSort
  ...ent of Physiology. It is part of MountainLab, a general framework for data analysis and visualization.
  3 KB (309 words) - 21:22, 6 December 2019
• TaxMaps
  ...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
  3 KB (321 words) - 15:45, 19 August 2022
• BDG-SeQuila
  ...computations are bread and butter for NGS analysis but the high volume of data make them execute very slowly or even failing to compute.
  3 KB (323 words) - 21:41, 26 August 2020
• Ngstools
  ...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
  5 KB (708 words) - 15:31, 14 December 2022
• Geomxngspipeline
  ...ts .dcc files, which can then be uploaded to the GeoMx DSP system for data analysis.
  3 KB (332 words) - 17:51, 29 January 2024
• ART
  ...benchmark a variety of method or tools for next-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation di
  3 KB (440 words) - 21:10, 6 December 2019
• SMRT-SV
  ...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
  3 KB (340 words) - 00:03, 22 August 2022
• Baypass
  ...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.]
  3 KB (355 words) - 21:05, 6 December 2019
• HUMAnN
  ...ther molecular functions from metagenomic or metatranscriptomic sequencing data.
  3 KB (327 words) - 14:26, 11 October 2022
• ClonalFrameML
  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
  3 KB (348 words) - 13:47, 15 August 2022
• Centrifuge
  ...r these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers
  3 KB (355 words) - 21:05, 6 December 2019
• MCScanX
  * 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.]
  3 KB (350 words) - 21:21, 6 December 2019
• ITK
  ...ys leading-edge algorithms for registering and segmenting multidimensional data.
  2 KB (339 words) - 19:04, 15 August 2022
• Guppy
  |{{#vardefine:url|https://nanoporetech.com/nanopore-sequencing-data-analysis}} Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies' basecall
  4 KB (506 words) - 21:07, 14 December 2022
• MMSEQ
  ...stom or haplotype-specific sequences. The latter allows haplotype-specific analysis, which is useful in studies of allelic imbalance. The posterior distributio
  3 KB (387 words) - 20:50, 18 August 2022
• Deepvariant
  ...eural network to call genetic variants from next-generation DNA sequencing data.
  3 KB (356 words) - 13:17, 16 April 2024
• Svtyper
  ...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.
  3 KB (360 words) - 14:04, 3 October 2022
• MZMine
  ...g, visualization and analysis of mass spectrometry based molecular profile data. It is based on the original MZmine toolbox described in 2006 Bioinformatic
  3 KB (417 words) - 13:28, 7 July 2023
• HLAminer
  ...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
  4 KB (541 words) - 14:55, 14 December 2022
• GenomicTools
  ...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
  3 KB (385 words) - 18:58, 12 August 2022
• SHEsisPlus
  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
  3 KB (344 words) - 15:04, 19 August 2022

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