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https://github.com/torognes/swipe

A software tool for performing rapid local alignment searches in amino acid or nucleotide sequence databases.

Proper citation: SWIPE (RRID:SCR_012771) Copy   

•   Source: SciCrunch Registry

http://sift.bii.a-star.edu.sg/

Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available.

Proper citation: SIFT (RRID:SCR_012813) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/lumi.html

Software that provides an integrated solution for the Illumina microarray data analysis.

Proper citation: lumi (RRID:SCR_012781) Copy   

•   Source: SciCrunch Registry

http://bioinf.comav.upv.es/ngs_backbone/index.html

A bioinformatic application created to work on sequence analysis by using NGS (Next Generation Sequencing) and sanger sequences.

Proper citation: Ngs backbone (RRID:SCR_012907) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/rqubic.html

This software package implements the QUBIC algorithm for the qualitative biclustering with gene expression data.

Proper citation: rqubic (RRID:SCR_012869) Copy   

•   Source: SciCrunch Registry

http://www.ema.europa.eu/

An agency responsible for the evaluation and supervision of medicines developed by pharmaceutical companies for use in the European Union. Its main responsibility is the protection and promotion of public and animal health through the evaluation and supervision of medicines for human and veterinary use. The Agency also plays a role in stimulating innovation and research in the pharmaceutical sector. The Agency gives scientific advice and other assistance to companies for the development of new medicines. It publishes guidelines on quality-, safety- and efficacy-testing requirements. A dedicated SME Office provides special assistance to small and medium-sized enterprises.

Proper citation: European Medicines Agency (RRID:SCR_011215) Copy   

•   Source: SciCrunch Registry

http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html

Software tool as a framework for modeling the sequences of short sequence motifs based on the maximum entropy principle (MEP). Used for sequence motifs such as those involved in RNA splicing.

Proper citation: MAxEntScan (RRID:SCR_016707) Copy   

•   Source: SciCrunch Registry

https://www.agilent.com/en/products/software-informatics/masshunter-suite/masshunter-qualitative-analysis-gcms

Software tools for compound-centric data mining and navigation. Used to identify compounds in overlapping and co-eluting peaks with feature extraction and correlation algorithms for chromatographic separation. Used for separating true signals from noise.

Proper citation: Agilent MassHunter WorkStation - Qualitative Analysis for GC/MS (RRID:SCR_016657) Copy   

•   Source: SciCrunch Registry

https://www.omicsnet.ca/

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   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/tools/vecscreen/

Software tool to screen a nucleic acid sequence for vector contamination. Detects foreign DNAs such as vector, linker, adapter, and primer regions involved in nucleotide sequences by using blast search against vector sequence database. The main unit of this tool is vecscreen program obtainable from NCBI.

Proper citation: VecScreen (RRID:SCR_016577) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/ConsensusClusterPlus.html

Software written in R for determining cluster count and membership by stability evidence in unsupervised analysis. Provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset with item tracking, item consensus and cluster consensus plots.

Proper citation: ConsensusClusterPlus (RRID:SCR_016954) Copy   

•   Source: SciCrunch Registry

https://www.schrodinger.com/ligprep

Software tool to correct and optimize the ligands by generating different protonation states, stereochemistry, tautomers, and ring conformations. Used to generate accurate, energy minimized 3D molecular structures.

Proper citation: Ligprep (RRID:SCR_016746) Copy   

•   Source: SciCrunch Registry

https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome

Software to generate phased, whole genome de novo assemblies from a Chromium prepared library. Used to create true diploid de novo assemblies and can separate homologous chromosomes over long distances.

Proper citation: Supernova assembler (RRID:SCR_016756) 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

https://www.schrodinger.com/epik

Software program for pKa prediction and protonation state generation for drug like molecules.

Proper citation: Epik (RRID:SCR_016745) Copy   

•   Source: SciCrunch Registry

https://github.com/BlaisProteomics/mzStudio

Software tool for proteomics data analysis, visualization, and notebook application. Dynamic digital canvas for user driven interrogation of mass spectrometry data. Operating system Unix/Linux, Windows.

Proper citation: mzStudio (RRID:SCR_017088) Copy   

•   Source: SciCrunch Registry

https://omictools.com/metacell-tool

Software package for single cell RNA-seq data analysis using k-NN graph partitions. Used to analyze group of scRNA profiles that are highly similar and provides features for deriving them. Can be used with large datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Metacell (RRID:SCR_017013) Copy   

•   Source: SciCrunch Registry

https://omicssimla.sourceforge.io

Software tool for generating multi omics data with disease status. Simulates genomics (SNPs and copy number variations), epigenomics ( whole genome bisulphite sequencing), transcriptomics ( RNA seq), and proteomics (normalized reverse phase protein array) data at the whole genome level. Available as desktop and web application version.

Proper citation: OmicsSIMLA (RRID:SCR_017011) Copy   

•   Source: SciCrunch Registry

https://inutano.github.io/cwl-metrics/

Software framework to collect and analyze computational resource usage of workflow runs based on common workflow language CWL. Used to share set of tools packaged in containers. Enables users to choose proper cloud instance for workflow runs based on run time metrics data. Operating system Unix/Linux.

Proper citation: cwl-metrics (RRID:SCR_017076) Copy   

•   Source: SciCrunch Registry