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http://home.uchicago.edu/~jiezhou/replication/

Source code providing a cost-effectiveness metric for guiding the design of large-scale RNA-seq differentially expressed (DE) studies.

Proper citation: AnalyzeReplication (RRID:SCR_012030) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/staden/

A C software implementation of SAM, BAM and CRAM file I/O.

Proper citation: Scramble (RRID:SCR_012036) Copy   

•   Source: SciCrunch Registry

http://mzmatch.sourceforge.net/mzmatch.R/mzmatch.ipeak.align.CowCoda.html

Software that performs retention time alignment on the given set of peaks.

Proper citation: CowCoDA (RRID:SCR_012039) Copy   

•   Source: SciCrunch Registry

http://obi-warp.sourceforge.net/

Software that aligns matrices along a single axis using Dynamic Time Warping (DTW) and a one-to-one (bijective) interpolated warp function.

Proper citation: OBI-Warp (RRID:SCR_012041) Copy   

•   Source: SciCrunch Registry

http://open-ms.sourceforge.net/

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on May 23rd,2023. Software that provides a set of computational tools which can be easily combined into analysis pipelines even by non-experts and can be used in proteomics workflows.

Proper citation: TOPP (RRID:SCR_012044) Copy   

•   Source: SciCrunch Registry

http://open-ms.sourceforge.net/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23rd,2023. Software that combines Lagrangian relaxation for solving an integer linear programming formulation with an adaptation of Yen''s k shortest paths algorithm.

Proper citation: Antilope (RRID:SCR_012046) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/swisspit/

Software for pipelined analysis of mass spectrometry data.

Proper citation: swissPIT (RRID:SCR_012045) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/icplquant/

A proteomics software tool for quantitatively analyzing large mass spectrometric datasets acquired from ICPL based proteomics experiments.

Proper citation: ICPL ESIQuant (RRID:SCR_012047) Copy   

•   Source: SciCrunch Registry

http://quantbio-tools.princeton.edu/cgi-bin/COALESCE

Software that can use large collections of genomic data and Bayesian integration to predict coregulated gene modules, the conditions of regulation, and the consensus binding motifs for regulation.

Proper citation: COALESCE (RRID:SCR_012005) Copy   

•   Source: SciCrunch Registry

http://bioinfo-out.curie.fr/projects/snp_gap/

Software for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured by single-nucleotide polymorphism (SNP) arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles. The method performs well even for poor-quality data, low tumor content, and highly rearranged tumor genomes.

Proper citation: Genome Alteration Print (RRID:SCR_012016) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.11/bioc/html/easyRNASeq.html

Software that calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as ''RPKM'' or by the ''DESeq'' or ''edgeR'' package.

Proper citation: easyRNASeq (RRID:SCR_012020) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mtoolbox/

Software for a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data.

Proper citation: MToolBox (RRID:SCR_012112) Copy   

•   Source: SciCrunch Registry

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

A user-friendly software tool to estimate allele-specific gene expression.

Proper citation: Allim (RRID:SCR_012114) Copy   

•   Source: SciCrunch Registry

http://revister.sourceforge.net/

Software for an automated pipeline using a ''local mapping reference reconstruction method'' to revise mismapped or partially misaligned reads at simple tandem repeat loci.

Proper citation: ReviSTER (RRID:SCR_012113) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/virtools/

Software for a low frequency Virus Variant detection pipeline for Illumina data.

Proper citation: VirVarSeq (RRID:SCR_012116) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/pegasus-fus/

Software that annotates biologically functional gene fusion candidates.

Proper citation: Pegasus-fus (RRID:SCR_012118) Copy   

•   Source: SciCrunch Registry

https://github.com/WaveCNV

Cancer specific CNV caller for Next Generation sequence.

Proper citation: WaveCNV (RRID:SCR_012244) Copy   

•   Source: SciCrunch Registry

https://github.com/BEETL/BEETL

Software tool as data transformation algorithm that restructures data in such a way that the transformed message is more compressible. Used for large scale compression of genomic sequence databases.

Proper citation: Burrows-Wheeler transform (RRID:SCR_012304) Copy   

•   Source: SciCrunch Registry

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

Software that implements some population genetics tests and estimators that can be applied to pooled sequences from Next Generation Sequencing experiments.

Proper citation: npstat (RRID:SCR_012128) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/nailsystemsbiology/

A set of software tools to simplify the range of computational activities involved in regulatory network inference. It is technology-independent and includes an interface layer to allow easy integration of components into other applications. It is implemented in MATLAB and is available for all researchers to use.

Proper citation: NAIL (RRID:SCR_012134) Copy   

•   Source: SciCrunch Registry