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https://code.google.com/p/automotifserver/
Software that predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences. The source code and precompiled binaries of brainstorming tool are available under Apache licensing.
Proper citation: AMS (RRID:SCR_012140) Copy
http://sourceforge.net/projects/phosphosite/
A bioinformatical software tool for analyzing (quantitative) phosphoproteome datasets. The program retrieves kinase-substrate predictions from NetworKIN and contains various statistical modules for futher analysis.
Proper citation: PhosphoSiteAnalyzer (RRID:SCR_012142) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/DNAcopy.html
Software that segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number.
Proper citation: DNAcopy (RRID:SCR_012560) Copy
Software suite of automated docking tools. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure. AutoDock consist of AutoDock 4 and AutoDock Vina. AutoDock 4 consists of autodock to perform docking of ligand to set of grids describing target protein, and autogrid to pre calculate these grids.
Proper citation: AutoDock (RRID:SCR_012746) Copy
https://github.com/bedops/bedops
A suite of tools to address common questions raised in genomic studies - mostly with regard to overlap and proximity relationships between data sets.
Proper citation: BEDOPS (RRID:SCR_012865) Copy
http://bioinf.wehi.edu.au/featureCounts/
A read summarization program, which counts mapped reads for the genomic features such as genes and exons.
Proper citation: featureCounts (RRID:SCR_012919) Copy
http://bioconductor.org/packages/release/bioc/html/DEXSeq.html
Software package focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.
Proper citation: DEXSeq (RRID:SCR_012823) Copy
Software tool that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Currently over 56% of human genomic sequence is identified and masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including nhmmer, cross_match, ABBlast/WUBlast, RMBlast and Decypher. RepeatMasker makes use of curated libraries of repeats and currently supports Dfam ( profile HMM library ) and RepBase ( consensus sequence library ).
Proper citation: RepeatMasker (RRID:SCR_012954) Copy
http://bioconductor.org/packages/release/bioc/html/DNaseR.html
A R package that enables the identification of protein binding footprints in DNase I hypersensitive sites sequencing (DNase-seq) data.
Proper citation: DNaseR (RRID:SCR_012819) Copy
http://sourceforge.net/projects/acaciaerrorcorr/?source=navbar
Accurate error-correction of amplicon pyrosequences.
Proper citation: Acacia (RRID:SCR_012896) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/charm.html
Software package that implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol.
Proper citation: charm (RRID:SCR_012992) Copy
http://trinityrnaseq.sourceforge.net/
Software for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
Proper citation: Trinity (RRID:SCR_013048) Copy
https://github.com/brentp/methylcode
A single program that takes of bisulfite-treated reads and outputs per-base methylation data.
Proper citation: MethylCoder (RRID:SCR_012997) Copy
http://sourceforge.net/projects/lofreq/
A fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data.
Proper citation: LoFreq (RRID:SCR_013054) Copy
http://sourceforge.net/projects/genecounter/
A computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression of eukaryotes, prokaryotes, as well as organisms with no available genome reference sequence.
Proper citation: GENE-counter (RRID:SCR_013056) Copy
http://sourceforge.net/projects/cloudaligner/
A map/reduce based application for mapping short reads generated by the next-generation sequencing machines.
Proper citation: CloudAligner (RRID:SCR_012962) Copy
http://sourceforge.net/projects/tracetuner/
Software tool for base and quality calling of trace files from DNA sequencing instruments.
Proper citation: TraceTuner (RRID:SCR_013019) Copy
http://sourceforge.net/projects/seqminer/
Software for a genome wide mapping data interpretation platform for NGS (ChIPSeq).
Proper citation: seqMINER (RRID:SCR_013020) Copy
http://bioconductor.org/packages/2.12/bioc/html/cn.mops.html
A data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data.
Proper citation: cn.mops (RRID:SCR_013036) Copy
http://sammate.sourceforge.net/
An open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate.
Proper citation: SAMMate (RRID:SCR_013037) Copy
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