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http://sourceforge.net/projects/amos/
A collection of tools and class interfaces for the assembly of DNA reads.
Proper citation: AMOS (RRID:SCR_013067) Copy
http://aluru-sun.ece.iastate.edu/doku.php?id=reptile
A software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing platforms.
Proper citation: Reptile (RRID:SCR_013075) Copy
http://www.guidetopharmacology.org
Portal and searchable database of pharmacological information. Information is presented at two levels, the initial view or landing pages for each target family provide expert-curated overviews of the key properties and the available selective ligands and tool compounds. For selected targets, more detailed introductory chapters for each family are available along with curated information on the pharmacological, physiological, structural, genetic and pathophysiogical properties of each target.
Proper citation: IUPHAR/BPS Guide to Pharmacology (RRID:SCR_013077) Copy
http://microbiomeutil.sourceforge.net/#A_CS
A chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp).
Proper citation: ChimeraSlayer (RRID:SCR_013283) Copy
http://sourceforge.net/projects/telescoper/
An algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework.
Proper citation: Telescoper (RRID:SCR_013206) Copy
http://alumni.cs.ucr.edu/~liw/isolasso.html
An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.
Proper citation: IsoLasso (RRID:SCR_013176) Copy
http://sourceforge.net/projects/heuraa/
Software for accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.
Proper citation: HeurAA (RRID:SCR_013212) 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://bioinfo.ctb.pku.edu.cn/MAP/
This resource is out of service. Documented on February 23,2021. Software for de novo metagenomic assembly program for shotgun DNA reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MAP (RRID:SCR_013216) Copy
http://genetics.bwh.harvard.edu/pph2/
Software tool which predicts possible impact of amino acid substitution on structure and function of human protein using straightforward physical and comparative considerations. PolyPhen-2 is new development of PolyPhen tool for annotating coding nonsynonymous SNPs.
Proper citation: PolyPhen: Polymorphism Phenotyping (RRID:SCR_013189) Copy
https://github.com/sorgerlab/ashlar
Software for image processing of cyclic immunofluorescence data. It performs alignment by simultaneous harmonization of layer/adjacency registration.
Proper citation: ASHLAR (RRID:SCR_016266) Copy
Software as an open source machine learning framework for everyone. Library for high performance numerical computation. Allows deployment of computation across a variety of platforms (CPUs, GPUs, TPUs), and from desktops to clusters of servers to mobile and edge devices.
Proper citation: tensorflow (RRID:SCR_016345) Copy
https://www.ebi.ac.uk/metagenomics/
Portal for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. Provides functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive (ENA).Microbiome analysis resource in 2020.
Proper citation: MGnify (RRID:SCR_016429) Copy
https://www.ncbi.nlm.nih.gov/geo/info/geo2r.html
Software as an interactive web tool to compare two or more groups of samples in a Gene Expression Omnibus (GEO) series regardless of data type and quality. Used to identify genes that are differentially expressed across experimental conditions. Results are presented as a table of genes ordered by significance.
Proper citation: GEO2R (RRID:SCR_016569) Copy
https://omictools.com/splicing-express-tool
Software suite for Alternative Splicing Events (ASEs) analysis from transcriptome sequencing data in any transcriptome. Used for identification, annotation and visualization. Written in Perl and suitable to run only in UNIX-like systems.
Proper citation: Splicing Express (RRID:SCR_016498) Copy
https://github.com/PF2-pasteur-fr/SARTools
Software package as a DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data.
Proper citation: SARTools (RRID:SCR_016533) Copy
http://saclab.tamu.edu/essentiality/transit/
Software tool Python based and open source for statistical analysis of TnSeq data. Provides a graphical interface to three different statistical methods for analyzing TnSeq data capable of identifying essential genes in individual datasets as well as comparative analysis between conditions.
Proper citation: TRANSIT (RRID:SCR_016492) Copy
https://cran.r-project.org/web/packages/anocva/index.html
Software R package as a nonparametric statistical test to compare clustering structures with applications in functional magnetic resonance imaging data (fMRI). Used for analysis of cluster variability in the diagnosis of neuropsychological disorders.
Proper citation: ANOCVA (RRID:SCR_016719) Copy
Web application for integrated analysis and interactive visualization of RNA interference (RNAi) screening data.
Proper citation: CARD (RRID:SCR_016602) Copy
https://visrsoftware.github.io/
Software as an R-based visual framework for analysis of sequencing datasets. Provides a framework for integrative and interactive analyses.
Proper citation: VisR (RRID:SCR_016658) Copy
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