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http://amp.pharm.mssm.edu/X2K/
Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures.
Proper citation: eXpression2Kinases (RRID:SCR_016307) Copy
https://cibersort.stanford.edu/
Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets.
Proper citation: CIBERSORT (RRID:SCR_016955) Copy
https://data.broadinstitute.org/alkesgroup/Eagle/
Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.
Proper citation: Eagle (RRID:SCR_015991) Copy
Software that contiguates (align, order, orientate), visualizes and designs primers to close gaps on shotgun assembled contigs based on a reference sequence. ABACAS finds alignment positions and identifies syntenies of assembled contigs against the reference, then generates a pseudomolecule taking overlapping contigs and gaps into account.
Proper citation: ABACAS (RRID:SCR_015852) Copy
Software package for p value based multiple testing that also implements dependence test and p-value simulation.
Proper citation: Myriads (RRID:SCR_017447) Copy
http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMAINATRIX
Software for protein domain search. It is a part of Embassy software package.
Proper citation: DOMAINATRIX (RRID:SCR_016084) Copy
https://git.metabarcoding.org/obitools/ecopcr/wikis/home
Software for Electronic PCR that estimates PCR barcode primers quality and develops new barcode primers. In conjunction with OBITools, users can postprocess ecoPCR output to compute barcode coverage and barcode specificity., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Ecopcr (RRID:SCR_016082) Copy
https://github.com/rbutleriii/Clinotator
Software that performs clinical interpretation of ambiguous ClinVar annotations. This software takes batches of variants as input and queries NCBI eutilities to generate scoring metrics.
Proper citation: Clinotator (RRID:SCR_016054) Copy
http://compbio.cs.princeton.edu/concavity/
Software for predicting protein ligand binding sites that integrate evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities. Used in predicting catalytic sites and drug binding pockets.
Proper citation: Concavity (RRID:SCR_016063) Copy
https://github.com/Pithikos/C-Thread-Pool
Software for minimal but powerful thread pool in ANSI C.
Proper citation: C Thread Pool (RRID:SCR_023999) Copy
https://github.com/smirarab/sepp/
Ensemble of HMM methods.Repository includes code for SEPP, TIPP, UPP, HIPPI. Methods use ensembles of Hidden Markov Models in different ways, each focusing on different problem.
Proper citation: sepp (RRID:SCR_024327) Copy
https://www.teuniz.net/edflib/
Software programming library for C/C++ to read/write EDF+/BDF+ files.It also reads old-type EDF/BDF files.
Proper citation: EDFlib (RRID:SCR_024010) Copy
http://www.dclunie.com/dicom3tools.html
Software package provides DICOM medical image files manipulation and conversion tools. Command line utilities for creating, modifying, dumping and validating DICOM files.
Proper citation: Dicom3tools (RRID:SCR_024008) Copy
https://github.com/stamatak/AxPcoords.dist
Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Faster than DistPCoA and numerically stable on large datasets.
Proper citation: AxPcoords (RRID:SCR_023971) Copy
http://sco.h-its.org/exelixis/web/software/AxParafit/index.html
Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Allows for rapid and much more thorough computation and analyses of large co-phylogenetic datasets.
Proper citation: AxParafit (RRID:SCR_023968) Copy
https://github.com/nextstrain/auspice
Web application for visualizing pathogen evolution.Interactive web app for visualizing phylogenomic data.
Proper citation: Auspice (RRID:SCR_023966) Copy
https://github.com/sanger-pathogens/assembly-stats
Software to get assembly statistics from FASTA and FASTQ files.
Proper citation: assembly-stats (RRID:SCR_023963) Copy
https://github.com/thegenemyers/DEXTRACTOR
Software as Bax file decoder and data compressor.
Proper citation: DEXTRACTOR (RRID:SCR_024005) Copy
https://github.com/nexml/nexml.java
Software repository contains java code for NeXML processing.
Proper citation: Java NeXML libraries and tools (RRID:SCR_024084) Copy
http://systemsbio.ucsd.edu/GoSurfer/
GoSurfer uses Gene Ontology (GO) information to analyze gene sets obtained from genome-wide computations or microarray analyses. GoSurfer is a graphical interactive data mining tool. It associates user input genes with GO terms and visualizes such GO terms as a hierarchical tree. Users can manipulate the tree output by various means, like setting heuristic thresholds or using statistical tests. Significantly important GO terms resulted from a statistical test can be highlighted. All related information are exportable either as texts or as graphics. Platform: Windows compatible
Proper citation: GoSurfer (RRID:SCR_005789) Copy
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