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https://savannah.gnu.org/projects/datamash/
Software for a command-line interface which performs basic numeric, textual and statistical operations on input textual data files. It is designed to aid researchers in automating analysis pipelines, without writing code or short scripts.
Proper citation: Datamash (RRID:SCR_016067) Copy
https://github.com/jts/nanopolish
Software package for signal-level analysis of Oxford Nanopore sequencing data.
Proper citation: Nanopolish (RRID:SCR_016157) 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 for syntax highlighting for computational biology.
Proper citation: bioSyntax (RRID:SCR_016207) Copy
https://odmltables.readthedocs.io
Software that facilitates the handling of metadata collections stored in the odML format. Some supported operations include reduction, merging of odml structures, and the conversion from the hierarchical odML format to tabular formats.
Proper citation: odMLtables (RRID:SCR_016228) 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://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
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
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
https://software.broadinstitute.org/gatk/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th,2023. Software package for genome analysis. Used for analysis of next generation genomic data in cancer.
Proper citation: IndelGenotyper (RRID:SCR_016663) Copy
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
Cloud based standardised European e-infrastructure for metabolomics and phenomics data processing, analysis and information mining on public or private cloud providers. Used for large scale computing for medical metabolomics.
Proper citation: PhenoMeNal (RRID:SCR_016605) Copy
https://niaid.github.io/spice/
Software application for data mining and visualization. Used for analyzes of large FLOWJO data sets from polychromatic flow cytometry and organizing the normalized data graphically.
Proper citation: SPICE (RRID:SCR_016603) Copy
Web based tool to create different types of molecular interaction networks and visually explore them in a three-dimensional (3D) space (genes/proteins, microRNAs, transcription factors or metabolites).
Proper citation: OmicsNet (RRID:SCR_016724) Copy
http://metascape.org/gp/index.html#/main/step1
Web service to analyze gene or protein lists. Provides automated meta analysis tools to understand pathways within a group of orthogonal target-discovery studies.
Proper citation: Metascape (RRID:SCR_016620) Copy
Computational biology resource for investigating candidate functional sites in eukarytic proteins. Functional sites which fit to the description linear motif are currently specified as patterns using Regular Expression rules. To improve the predictive power, context-based rules and logical filters are being developed and applied to reduce the amount of false positives. The current version of the ELM server provides core functionality including filtering by cell compartment, phylogeny, globular domain clash (using the SMART/Pfam databases) and structure. In addition, both the known ELM instances and any positionally conserved matches in sequences similar to ELM instance sequences are identified and displayed (see ELM instance mapper). Although the ELM resource contains a large collection of functional site motifs, the current set of motifs is not exhaustive.
Proper citation: Eukaryotic Linear Motif (RRID:SCR_003085) Copy
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