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https://github.com/flo-compbio/xlmhg
Software Python package as a semiparametric test for enrichment in ranked lists. Used for determining gene set enrichment.
Proper citation: XL-mHG (RRID:SCR_016846) Copy
https://github.com/PGB-LIV/VAPPER
Software tool for analysis of variant antigens in African trypanosomes. Used for quantitative analysis of antigenic diversity in systems data of genomes, transcriptomes, and proteomes, called Variant Antigen Profiling to understand how antigenic diversity relates to clinical outcome, how antigen genes may be used as epidemiological markers of virulence, and in measuring gene expression during experimental infections.
Proper citation: VAPPER (RRID:SCR_016993) Copy
https://github.com/CGATOxford/UMI-tools
Open source software package for handling Unique Molecular Identifiers in NGS data sets.
Proper citation: UMI-tools (RRID:SCR_017048) Copy
https://bioconductor.org/packages/release/bioc/html/goseq.html
Software application for performing Gene Ontology analysis on RNAseq data and other length biased data. Used to reduce complexity and highlight biological processes in genome wide expression studies.
Proper citation: Goseq (RRID:SCR_017052) Copy
https://github.com/fmaguire/Bridger_Assembler
Software package as de novo trascriptome assembler for RNA-Seq data. Framework for de novo transcriptome assembly using RNA-seq data. Can assemble all transcripts from short reads without using reference. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux.
Proper citation: Bridger (RRID:SCR_017039) Copy
https://github.com/dgrun/FateID
Software R package for inference of cell fate bias from single cell RNA-seq data. Iterative supervised learning algorithm for probabilistic quantification of cell fate bias in progenitor populations.
Proper citation: FateID (RRID:SCR_017244) Copy
https://github.com/powellgenomicslab/ascend
Software R package for analysis of single cell RNA-seq expression, normalization and differential expression data. Provides framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and visualization functions.
Proper citation: ascend (RRID:SCR_017257) Copy
Software tool as stochastic algorithm for estimating maximum likelihood phylogenies. Used for phylogenomic inference.
Proper citation: IQ-TREE (RRID:SCR_017254) Copy
http://research.mssm.edu/integrative-network-biology/Software.html
Software tool as probabilistic multi omics data matching procedure to curate data, identify and correct data annotation and errors in large databases. Used to check potential labeling errors in profiles where number of cis relationships is small, such as miRNA and RPPA profiles.
Proper citation: proMODMatcher (RRID:SCR_017219) Copy
https://github.com/SionBayliss/PIRATE
Software pangenomics toolbox for clustering diverged orthologues in bacteria. Used to identify and classify orthologous gene families in bacterial pangenomes over wide range of sequence similarity thresholds.
Proper citation: PIRATE (RRID:SCR_017265) Copy
Software tool for automated removal of spurious sequences or poorly aligned regions from multiple sequence alignment. Software package for automated alignment trimming in large scale phylogenetic analyses.
Proper citation: trimAl (RRID:SCR_017334) Copy
A tool for high-performance comparative metagenomics that allows users to view, query, browse, and compare metagenomics annotation profiles from short reads or assemblies. Users can use statistical tests, hierarchical clustering, multidimensional scaling, and heat maps to compare multiple datasets at various functional and taxonomic levels.
Proper citation: METAREP (RRID:SCR_011926) Copy
Software providing a data analysis pipeline for shotgun mass-spectrometry proteomics.
Proper citation: CPFP (RRID:SCR_012043) Copy
https://github.com/macs3-project/MACS
Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity.
Proper citation: MACS (RRID:SCR_013291) Copy
http://www.ngsbicocca.org/html/fusion_analyser.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2023. Software used to detect gene fusions from paired-end RNA-Seq data.
Proper citation: Fusion Analyser (RRID:SCR_000059) Copy
http://www.bioconductor.org/packages/release/bioc/html/metahdep.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies.
Proper citation: metahdep (RRID:SCR_001225) Copy
http://www.bioconductor.org/packages/release/bioc/html/pickgene.html
Software for adaptive Gene Picking for Microarray Expression Data Analysis.
Proper citation: pickgene (RRID:SCR_001331) Copy
https://github.com/hms-dbmi/spp
R analysis and processing package for Illumina platform Chip-Seq data.
Proper citation: SPP (RRID:SCR_001790) Copy
Statistical software tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. This software is optimized for analysis of whole-exome sequencing data and whole-genome sequencing data.
Proper citation: SNVer (RRID:SCR_002061) Copy
A software package that anayzes the structral details of RNA molecules through rapid quantification of a footprinting gel. By automating many of the steps involved in gel analysis, approximately one entire gel with thousands of bands can be quantified in less than 10 minutes using SAFA. In general, all the automated features have a manual override, such that even difficult or exceptional gels can be analyzed with the package.
Proper citation: SAFA Footprinting Software (RRID:SCR_002707) Copy
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