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

Software package for normalizing, diagnostics and visualization of NanoString nCounter data. Key features include an extensible environment for method comparison and new algorithm development, integrated gene and sample diagnostics, and facilitated downstream statistical analysis.

Proper citation: NanoStringNorm (RRID:SCR_003382) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/skewer/

Software program for adapter trimming that is specially designed for processing Illumina paired-end sequences.

Proper citation: skewer (RRID:SCR_001151) Copy   

•   Source: SciCrunch Registry

http://www.ch.embnet.org/software/COILS_form.html

COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation.

Proper citation: COILS: Prediction of Coiled Coil Regions in Proteins (RRID:SCR_008440) Copy   

•   Source: SciCrunch Registry

http://www.seqexpress.com/

A comprehensive analysis and visualization software package for gene expression experiments that provides: a number of clustering and analysis techniques; integrated gene expression and analysis result visualizations, integration with the Gene Expression Omnibus; and an optional data sharing architecture. GO is used to assign functional enrichment scores to clusters, using a combination of specially developed techniques and general statistical methods. These results can be explored using the in built ontology browsing tool or through the generated web pages. SeqExpress also supports numerous data transformation, projection, visualization, file export/import, searching, integration (with R), and clustering options.

Proper citation: SeqExpress (RRID:SCR_007075) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.13/bioc/html/epigenomix.html

Software package for the integrative analysis of microarray based gene expression and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types.

Proper citation: epigenomix (RRID:SCR_006407) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/soapaligner.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Updated version of SOAP software for short oligonucleotide alignment that features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SOAPaligner/soap2 (RRID:SCR_005503) Copy   

•   Source: SciCrunch Registry

http://subread.sourceforge.net/

Software package for high-performance read alignment, quantification and mutation discovery.General purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. Subread aligner as fast, accurate and scalable read mapping by seed-and-vote.These programs were also implemented in Bioconductor R package Rsubread.

Proper citation: Subread (RRID:SCR_009803) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/gsa-snp/

A tool for the gene-set (or pathway) analysis of a genome-wide association study result. It accepts a genome-wide list of SNPs and their association P-values. It summarizes the SNP P-values into nearby genes. The gene-by-gene summary results are then further summarized by gene-sets such as Gene Ontology, KEGG pathways, or user-created gene-sets. Various standardization and statistical tests can be performed and the resulting gene-sets that pass a significance level after multiple-testing correction are reported. The tool is written in Java and is available as a standalone version.

Proper citation: GSA-SNP (RRID:SCR_013109) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/

Software tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data.

Proper citation: Trim Galore (RRID:SCR_011847) Copy   

•   Source: SciCrunch Registry

https://github.com/kendomaniac/docker4seq

Software R package to execute next generation sequencing computing applications, e.g. reads mapping and counting, wrapped in docker containers.

Proper citation: docker4seq (RRID:SCR_017006) Copy   

•   Source: SciCrunch Registry

https://www.ruhr-uni-bochum.de/mpc/software/ProCon/index.html.en

Java based conversion tool for conversion of data from Proteomics files or a LIMS (Laboratory Information Management System) database into standard formats. Used to support wet-lab scientists in creating proteomics data files ready for upload into the public repositories.

Proper citation: ProCon - PROteomics CONversion (RRID:SCR_016363) Copy   

•   Source: SciCrunch Registry

https://github.com/mandricigor/ScaffMatch

Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes.

Proper citation: ScaffMatch (RRID:SCR_017025) Copy   

•   Source: SciCrunch Registry

https://github.com/isovic/racon

Software tool as de novo genome assembly from long uncorrected reads. Used to correct raw contigs generated by rapid assembly methods which do not include consensus step. Supports data produced by Pacific Biosciences and Oxford Nanopore Technologies.

Proper citation: Racon (RRID:SCR_017642) Copy   

•   Source: SciCrunch Registry

https://github.com/almorlio/CiLiQuant

Software tool to separate junction reads based on their linear or circular origin. Only non ambiguous junction reads are used to compare relative linear and circular transcript abundance.

Proper citation: CiLiQuant (RRID:SCR_019319) Copy   

•   Source: SciCrunch Registry

https://github.com/taborlab/FlowCal

Open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units. Can be run using intuitive Microsoft Excel interface, or customizable Python scripts. Software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Automatically gates data, calculates common statistics, and produces plots.

Proper citation: FlowCal (RRID:SCR_018140) Copy   

•   Source: SciCrunch Registry

https://github.com/ComparativeGenomicsToolkit/hal/tree/master/synteny

Software tool as conserved synteny block construction method for multiple whole-genome alignments. Implementation of DAG-based for reconstruction of synteny blocks from genome alignment.

Proper citation: halSynteny (RRID:SCR_018127) Copy   

•   Source: SciCrunch Registry

http://metap.helmholtz-muenchen.de/metap2/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 5,2023. Software tool for processing in metabolomics experiments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MetaP (RRID:SCR_014686) Copy   

•   Source: SciCrunch Registry

https://github.com/nbcrrolls/workflows/tree/master/Production/AmberGPUMDSimulation

A workflow for running molecular dynamics simulations. It can be used for all-atom molecular dynamic simulations, which involve five steps of minimization, one step of heating, three steps of equilibration, and one or more instances of production. The input is a set of directories that include the MD simulation input scripts, system topology and coordinate files. Output files are list of plots, simulation trajectories, intermediate files, restart files, and the like.

Proper citation: Molecular Dynamics Workflow (BioKepler) (RRID:SCR_014389) Copy   

•   Source: SciCrunch Registry

https://github.com/jstjohn/SimSeq

An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries .

Proper citation: SimSeq (RRID:SCR_006947) Copy   

•   Source: SciCrunch Registry

http://mutpred.mutdb.org/

Web application tool developed to classify an amino acid substitution as disease-associated or neutral in human.

Proper citation: MutPred (RRID:SCR_010778) Copy   

•   Source: SciCrunch Registry