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https://github.com/BenLangmead/bsmooth-align

Software statistics and alignment pipeline that performs the alignment of bisulfite sequence reads and tabulates read-level methylation measurements.

Proper citation: BSmooth-align (RRID:SCR_000013) Copy   

•   Source: SciCrunch Registry

http://srf.sourceforge.net/

A generic format for DNA sequence data. The primary motivation for creating SRF has been to enable a single format capable of storing data generated by any DNA sequencing technology.

Proper citation: Sequence Read Format (RRID:SCR_000132) Copy   

•   Source: SciCrunch Registry

http://dock.compbio.ucsf.edu/

An algorithm used to predict and analyse binding modes of docking molecules. Users can search ligand databases for compounds that inhibit enzymatic activity and bind to particular molecules and nucleic acid targets. Molecular docking is used to predict a predominant binding mode(s) of a ligand in three-dimensional structure. This method can be used for molecular biology and computer-assisted drug design.

Proper citation: DOCK (RRID:SCR_000128) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/exomesuite/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software application designed to analyze variant call files from next generation sequencing data to identify variants causing disease.

Proper citation: exomeSuite (RRID:SCR_000129) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/data/annotation/html/RmiR.Hs.miRNA.html

Software package for various databases of microRNA Targets.

Proper citation: RmiR.Hs.miRNA (RRID:SCR_000101) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/nfuse/

Software that predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole Genome Shotgun Sequencing (WGSS).

Proper citation: nFuse (RRID:SCR_000066) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/gasv/

Software tool for identifying structural variants (SVs) from paired-end sequencing data.GASV distribution includes three components that are typically run in succession: the BAM file of unique paired-read mappings is processed; structural variants are identified by clustering discordant fragments; and a probabilistic algorithm improves the specificity of GASV predictions.

Proper citation: GASV (RRID:SCR_000061) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/chipmeta/

Software using a Hierarchical hidden Markov model for jointly analyzing ChIP-chip and ChIP-seq datasets.

Proper citation: ChIPmeta (RRID:SCR_000054) Copy   

•   Source: SciCrunch Registry

https://github.com/SciLifeLab/facs

Software for classification of Sequences using Bloom filters that can accurately and rapidly align sequences to a reference sequence.

Proper citation: FACS (RRID:SCR_000055) Copy   

•   Source: SciCrunch Registry

https://github.com/common-workflow-language/cwltool

Reference implementation of the Common Workflow Language standards. It provides complete features and tools and comprehensive validation of CWL. The reference implementation consists of two packages. The cwltool package is the primary Python module containing the reference implementation in the cwltool module and console executable by the same name. The cwlref-runner package is optional and provides an additional entry point under the alias cwl-runner, which is the implementation-agnostic name for the default CWL interpreter installed on a host.

Proper citation: cwltool (RRID:SCR_015528) Copy   

•   Source: SciCrunch Registry

http://mirwalk.umm.uni-heidelberg.de/

Software tool to store the predicted and the experimentally validated microRNA (miRNA)-target interaction pairs. Predictions within the complete sequence of genes of human, mouse, and rat genomes. Integrates a comparative platform of miRNA-binding sites resulting from ten different prediction datasets.

Proper citation: miRWalk (RRID:SCR_016509) Copy   

•   Source: SciCrunch Registry

http://www.clcbio.com/products/clc-main-workbench/

A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management.

Proper citation: CLC Main Workbench (RRID:SCR_000354) Copy   

•   Source: SciCrunch Registry

http://nucleobytes.com/index.php/4peaks

Software application for viewing and editing sequence trace files.

Proper citation: 4Peaks (RRID:SCR_000015) Copy   

•   Source: SciCrunch Registry

https://mzmatch.sourceforge.net/MetAssign.php

Software that combines information from the mass-to-charge ratio, retention time and intensity of each peak, together with a model of the inter-peak dependency structure, to increase the accuracy of peak annotation. The software has been implemented as part of the mzMatch metabolomics analysis pipeline, which is available for download.

Proper citation: MetAssign (RRID:SCR_000092) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/metaMA/

Software R package for meta-analysis for microarrays. It combines either p-values or modified effect sizes from different studies to find differentially expressed genes.

Proper citation: metaMA (RRID:SCR_000408) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/annotare/

A software tool for annotating biomedical investigations and the resulting data, then producing a MAGE-TAB file. This software is a standalone desktop which features: an editor function, an annotation modifier, incorporation of terms from biomedical ontologies, standard templates for common experiment types, a design aid to help create a new document, and a validator that checks for syntactic and semantic violations.

Proper citation: Annotare (RRID:SCR_000319) Copy   

•   Source: SciCrunch Registry

http://apps.cytoscape.org/apps/pepper

A Cytoscape app designed to identify protein pathways / complexes as densely connected subnetworks from seed lists of proteins derived from pull-down assays (i.e AP-MS...).

Proper citation: PEPPER (RRID:SCR_000431) Copy   

•   Source: SciCrunch Registry

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https://cran.r-project.org/web/packages/adegenet/index.html

Software package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis. (entry from Genetic Analysis Software)

Proper citation: ADEGENET (RRID:SCR_000825) Copy   

•   Source: SciCrunch Registry

https://pypi.python.org/pypi/illuminate/

Python module and utilities to parse the metrics binaries output by Illumina sequencers, and provides usable data in the form of python dictionaries and dataframes. Intended to emulate the output of Illumina SAV, it allows you to print sequencing run metrics to the command line as well as work with the data programmatically.

Proper citation: Illuminate (RRID:SCR_000178) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ngs-cleaner/

Software application that provides cleaning of FASTQ/A formatted large DNA sequence files containing multiple short-reads sequences provided by Next Generation Sequencing platforms.

Proper citation: NGS-Cleaner (RRID:SCR_000574) Copy   

•   Source: SciCrunch Registry