Search results

• Mosaic
  ...nient handling and visualization of single-cell data to enable exploratory analysis.
  2 KB (282 words) - 14:15, 14 October 2021
• ClonalFrame
  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
  3 KB (349 words) - 18:33, 12 August 2022
• MOABS
  ...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.
  2 KB (291 words) - 19:53, 12 August 2022
• SeqyClean
  ...ary preparation. Such nucleotides can potentially case hurdles during data analysis and hereby need to be removed. In additional, the noise, which is presented
  3 KB (312 words) - 22:41, 21 August 2022
• AFNI
  ...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
  3 KB (363 words) - 20:52, 11 August 2022
• QAPA
  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.]
  3 KB (305 words) - 16:54, 15 January 2021
• Nsight
  ...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
  3 KB (316 words) - 20:39, 24 August 2022
• Data Science Platform
  [[Category:Data Science]][[Category:Help]] ...mputing provides essential infrastructure, tools, and expertise to support data science research and accelerate impactful discoveries. All support requests
  5 KB (663 words) - 19:52, 14 May 2024
• FSL
  ...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
  3 KB (365 words) - 16:47, 17 January 2023
• ETE3
  ...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:
  3 KB (400 words) - 19:13, 10 June 2022
• SPM
  ...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.
  3 KB (327 words) - 17:00, 13 February 2024
• Nimare
  ...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
  3 KB (343 words) - 15:27, 15 August 2022
• TrackVis/DTK
  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
  3 KB (418 words) - 14:56, 18 October 2022
• Methylpy
  Methylpy, a pyhton-based analysis pipeline for (single-cell) (whole-genome) bisulfite sequencing data
  3 KB (309 words) - 21:21, 6 December 2019
• NONMEM
  ...effects modelling tool used in population pharmacokinetic/pharmacodynamic analysis. ...in previous versions. NONMEM® can be used to simulate data as well as fit data.
  3 KB (439 words) - 21:23, 6 December 2019
• Ovito
  * 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
  3 KB (333 words) - 15:29, 1 December 2023
• Cytoscape
  ...e core distribution provides a basic set of features for data integration, analysis, and visualization.
  3 KB (334 words) - 14:23, 15 August 2022
• Garfield
  ...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:
  3 KB (342 words) - 22:51, 30 November 2022
• MEGAN
  ...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
  3 KB (338 words) - 15:38, 15 April 2024
• Plink
  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
  3 KB (342 words) - 20:25, 12 August 2022
• MitoPhAST
  ...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.
  3 KB (382 words) - 14:27, 23 April 2020
• EQTLA
  ...orming both cis- and trans-eQTL analysis given a set of raw genetic marker data and expression values.
  2 KB (269 words) - 18:52, 12 August 2022
• QIIME2
  ...from representative sequences of OTUs, and through downstream statistical analysis, visualization, and production of publication-quality graphics. QIIME has b
  3 KB (435 words) - 15:15, 19 August 2022
• EEGLAB
  event-related EEG, MEG and other electrophysiological data using independent component analysis (ICA), time/frequency analysis, and other methods
  2 KB (271 words) - 14:56, 15 August 2022
• Gblocks
  prior to phylogenetic analysis. Gblocks selects blocks in a similar way as the final alignment more suitable for phylogenetic analysis. Gblocks outputs
  3 KB (441 words) - 13:56, 13 June 2022
• Rnalysis
  ...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.
  5 KB (648 words) - 16:12, 25 April 2023
• GrADS
  ...two data models for handling gridded and station data. GrADS supports many data file formats, including binary (stream or sequential), GRIB2, NetCDF, and H
  3 KB (334 words) - 20:26, 24 August 2022
• TRANSIT
  ...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
  2 KB (279 words) - 21:29, 6 December 2019
• EMBOSS
  ...integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercia
  3 KB (372 words) - 15:01, 15 August 2022
• FAST
  ...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)]
  3 KB (358 words) - 21:21, 6 December 2019
• Pomoxis
  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
  2 KB (285 words) - 18:48, 21 August 2022
• Biolite
  ...cks provenance, and provides lightweight tools for building out customized analysis pipelines. * A 'catalog' database for pairing metadata with and organizing NGS data files.
  3 KB (362 words) - 12:54, 15 August 2022
• RepeatExplorer
  uses high-throughput genome sequencing data as an input and performs graph-based clustering analysis of sequence read similarities to identify
  2 KB (278 words) - 21:44, 21 August 2022
• VDJtools
  ...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
  2 KB (280 words) - 21:29, 6 December 2019
• TREEPUZZLE
  ...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.]
  4 KB (450 words) - 19:31, 10 June 2022
• CellRanger-ARC
  ...erential analysis, and feature linkage between peaks and genes that aid in data interpretation.
  3 KB (288 words) - 18:24, 12 August 2022
• CGATools
  ...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
  2 KB (291 words) - 13:26, 15 August 2022
• Circos
  ...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
  3 KB (409 words) - 13:35, 15 August 2022
• Bactopia
  ...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.
  2 KB (292 words) - 21:38, 10 January 2023
• Rvtests
  ...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.]
  3 KB (293 words) - 21:59, 21 August 2022
• Biopieces
  ...downstream Biopieces until the data stream is terminated at the end of the analysis as outlined below: * BP_DATA - biopieces data directory
  3 KB (410 words) - 15:40, 10 December 2021
• BEAGLE
  ...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,
  5 KB (615 words) - 15:36, 14 December 2022
• QTLtools
  ...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.]
  2 KB (297 words) - 20:58, 21 August 2022
• Healthcare and Life Sciences
  ...science, including medical image analysis, disease detection, and genomic data interpretation, through [https://support.rc.ufl.edu/ support requests] or [ ...very that simplifies and accelerates the training of models using your own data and scaling the deployment of models for drug discovery applications.
  4 KB (521 words) - 16:00, 14 May 2024
• Biology
  ..., 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>.
  4 KB (665 words) - 21:23, 14 December 2022
• HTSeq
  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
  3 KB (411 words) - 19:05, 12 August 2022
• Lima
  ...ltiplexing. This new tool provides a better end-to-end user experience for analysis of multiplexed samples.
  3 KB (299 words) - 19:57, 15 August 2022
• Gephi
  ...ecognized to facilitate reasoning. This is a software for Exploratory Data Analysis, a paradigm appeared in the Visual Analytics field of research.
  3 KB (337 words) - 17:42, 11 January 2023
• CellRanger
  ...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
  2 KB (294 words) - 18:24, 12 August 2022
• RepeatAnalysisTools
  This repository contains instructions for processing and repeat analysis of sequence data generated with the PacBio No-Amp Targeted Sequencing
  4 KB (430 words) - 16:55, 15 December 2022

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