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https://github.com/lh3/fermi-lite

Standalone C library as well as a command-line tool for assembling Illumina short reads in small regions. It is an overlap-based assembler used in sequencing to retain heterozygous events and to assemble diploid regions for the purpose of variant calling.

Proper citation: fermi-lite (RRID:SCR_016112) Copy   

•   Source: SciCrunch Registry

http://omics.informatics.indiana.edu/AbundantOTU/

Software tool for analysis of large 16S rRNA pyrosequences by using a consensus alignment algorithm, utilizing the sequence redundancy of abundant species in the pyrosequence dataset.

Proper citation: AbundantOTU+ (RRID:SCR_016527) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/biobakery/biobakery/wiki/Home

Analysis environment and collection of individual software tools to process raw shotgun metagenome or metatranscriptome sequencing data for quantitative microbial community profiling. Used for a metaomics data analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: biobakery (RRID:SCR_016596) Copy   

•   Source: SciCrunch Registry

http://www.lincsproject.org/

Project to create network based understanding of biology by cataloging changes in gene expression and other cellular processes when cells are exposed to genetic and environmental stressors. Program to develop therapies that might restore pathways and networks to their normal states. Has LINCS Data Coordination and Integration Center and six Data and Signature Generation Centers: Drug Toxicity Signature Generation Center, HMS LINCS Center, LINCS Center for Transcriptomics, LINCS Proteomic Characterization Center for Signaling and Epigenetics, MEP LINCS Center, and NeuroLINCS Center.

Proper citation: LINCS Project (RRID:SCR_016486) Copy   

•   Source: SciCrunch Registry

http://marrvel.org/

Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research.

Proper citation: MARRVEL (RRID:SCR_016871) Copy   

•   Source: SciCrunch Registry

https://software.broadinstitute.org/software/discovar/blog/

Software tool for variant calling with reference and de novo assembly of genomes. The heart of DISCOVAR is a de novo genome assembler which can generate de novo assemblies for both large and small genomes.

Proper citation: Discovar assembler (RRID:SCR_016755) Copy   

•   Source: SciCrunch Registry

https://github.com/PathwayAnalysisPlatform/PathwayMatcher

Software tool for multi omics pathway mapping and proteoform network generation. Open source software writen in Java to search for pathways related to a list of proteins in Reactome.

Proper citation: PathwayMatcher (RRID:SCR_016759) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/GenomicFeatures/

Software R package for making and manipulating transcript centric annotations. Used to download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database.

Proper citation: GenomicFeatures (RRID:SCR_016960) Copy   

•   Source: SciCrunch Registry

https://github.com/schatzlab/genomescope

Open source software package for fast genome analysis from unassembled short reads. Used to estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach.

Proper citation: GenomeScope (RRID:SCR_017014) Copy   

•   Source: SciCrunch Registry

https://pachterlab.github.io/sleuth/about

Software tool for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto. Used for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance.

Proper citation: sleuth (RRID:SCR_016883) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/GenomicRanges/

Software R package for computing and annotating genomic ranges. Used for storing and manipulating genomic intervals and variables defined along genome.

Proper citation: Genomic Ranges (RRID:SCR_017051) Copy   

•   Source: SciCrunch Registry

https://combine-lab.github.io/salmon/

Software tool for quantifying expression of transcripts using RNA-seq data. Provides fast and bias-aware quantification of transcript expression. Transcriptome-wide quantifier to correct for fragment GC-content bias.

Proper citation: Salmon (RRID:SCR_017036) Copy   

•   Source: SciCrunch Registry

https://panoramaweb.org/project/home/begin.view?

Repository software for targeted mass spectrometry assays from Skyline. Targeted proteomics knowledge base. Public repository for quantitative data sets processed in Skyline. Facilitates viewing, sharing, and disseminating results contained in Skyline documents.

Proper citation: PanoramaWeb (RRID:SCR_017136) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/aidenlab/juicer.git

Software platform for analyzing kilobase resolution Hi-C data. Open source tool for analyzing terabase scale Hi-C datasets. Allowes to transform raw sequence data into normalized contact maps.

Proper citation: Juicer (RRID:SCR_017226) Copy   

•   Source: SciCrunch Registry

https://github.com/YosefLab/FastProject

Software Python tool for low dimensional analysis of single-cell RNA-Seq data. Software package for two dimensional visualization of single cell data. Analyzes gene expression matrix and produces output report in which two-dimensional of data can be explored.

Proper citation: FastProject (RRID:SCR_017462) Copy   

•   Source: SciCrunch Registry

http://pathwaynet.princeton.edu/

Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks.

Proper citation: PathwayNet (RRID:SCR_017353) Copy   

•   Source: SciCrunch Registry

https://github.com/brentp/peddy

Software package that evaluates correspondence between stated sexes, relationships, and ancestries in pedigree file and those inferred from genotypes in VCF file resulting from human whole genome sequencing or whole exome sequencing studies. Facilitates both automated and interactive, visual detection of sample swaps, poor sequencing quality, and other indicators of sample problems.

Proper citation: peddy (RRID:SCR_017287) Copy   

•   Source: SciCrunch Registry

http://topaz.gatech.edu/GeneMark/

Software package for ab initio identification of protein coding regions in RNA transcripts. Algorithm parameters are estimated by unsupervised training which makes unnecessary manually curated preparation of training sets. Sets of assembled eukaryotic transcripts can be analyzed by modified GeneMarkS-T algorithm which part of gene prediction programs GeneMark.

Proper citation: GeneMarkS-T (RRID:SCR_017648) Copy   

•   Source: SciCrunch Registry

https://pachterlab.github.io/cgal/

Software tool for computing genome assembly likelihoods.Computes likelihood of reads with respect to assembly and statistical model which can be used as metric for evaluating assemblies. Novel likelihood based approach to assembly assessment in absence of ground truth.

Proper citation: Computing Genome Assembly Likelihoods (RRID:SCR_017624) Copy   

•   Source: SciCrunch Registry