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http://sourceforge.net/projects/protms/
A software tool for the proteomics community that may help improving analysis of proteomic experimental data.
Proper citation: Quant (RRID:SCR_000267) Copy
http://peptideprophet.sourceforge.net/
Software that automatically validates peptide assignments to MS/MS spectra made by database search programs such as SEQUEST.
Proper citation: PeptideProphet (RRID:SCR_000274) Copy
https://github.com/GregoryFaust/samblaster
Software tool to mark duplicates and extract discordant and split reads from SAM files. This fast and flexible program for marking duplicates in read-id grouped paired-end SAM files can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.
Proper citation: SAMBLASTER (RRID:SCR_000468) Copy
https://code.google.com/p/snavi/
Desktop application for analysis and visualization of large-scale cell signaling networks.
Proper citation: SNAVI (RRID:SCR_000091) Copy
http://sourceforge.net/projects/ngsrich/
Software for target enrichment performance for next-generation sequencing.
Proper citation: NGSrich (RRID:SCR_001333) Copy
https://github.com/uci-cbcl/PyLOH
Software for deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity. The model resolves the identifiability problem by integrating two types of sequencing information - somatic copy number alterations and loss of heterozygosity - within an unified probabilistic framework.
Proper citation: PyLOH (RRID:SCR_001511) Copy
https://github.com/JialiUMassWengLab/TEMP
Software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data.
Proper citation: TEMP (RRID:SCR_001788) Copy
http://kirchnerlab.github.io/libmgf/
A flex/bison-based C++ Mascot Generic Format (MGF) parser library.
Proper citation: libmgf (RRID:SCR_002664) Copy
https://github.com/rcanovas/libCSAM
Contains several C++ codes for compress, decompress, and access each of the fields of any SAM format file.
Proper citation: libCSAM (RRID:SCR_002766) Copy
https://github.com/lh3/ropebwt2
A software tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pseudo-BWT position by position, starting from the end of the sequences. This algorithm can be largely considered a mixture of BCR and dynamic FM-index. Nonetheless, ropeBWT2 is unique in that it may implicitly sort the input into reverse lexicographical order (RLO) or reverse-complement lexicographical order (RCLO) while building the index.
Proper citation: RopeBWT2 (RRID:SCR_002673) Copy
http://cran.r-project.org/web/packages/pairheatmap/
A software tool to compare two heatmaps and discover patterns within and across groups. In the context of biology, group can be defined based on gene ontology.
Proper citation: pairheatmap (RRID:SCR_003109) Copy
https://github.com/quwubin/MFEprimer/
A fast thermodynamics-based software program for checking PCR primer specificity against genomic DNA and mRNA/cDNA sequence databases.
Proper citation: MFEprimer (RRID:SCR_003066) Copy
https://github.com/timflutre/eqtlbma/wiki
Software package that implements Bayesian statistical methods to detect eQTLs jointly in multiple subgroups (e.g. tissues). Key features are to borrow information across subgroups, to explicitly model heterogeneity (qualitatively and quantitatively), and to borrow information across genes to estimate hyper-parameters from the data (empirical Bayes).
Proper citation: eQtlBma (RRID:SCR_003102) Copy
https://github.com/CRG-Barcelona/bwtool/wiki
A command-line utility for bigWig files designed to read bigWig files rapidly and efficiently, providing functionality for extracting data and summarizing it in several ways, globally or at specific regions. Its functionality is subdivided into subprograms that roughly fall into three categories: data extraction, analysis, and data modification, although e.g. in the case of the matrix program or the sax program, the boundary between data extraction and analysis isn't very strong. The data modification programs all have the behavior that a bigWig is inputted and a new bigWig is outputted.
Proper citation: bwtool (RRID:SCR_003035) Copy
https://github.com/PacificBiosciences/DevNet/wiki/SMRT-View
An open source Genome Browser that visualizes data generated by PacBio Sequencing Systems. * Users can explore and interact with all types of analysis results, including resequencing, De novo, cDNA, and barcoding. * Users can also visualize base modifications, base identification and motifs analysis results.
Proper citation: SMRT View (RRID:SCR_003029) Copy
https://code.google.com/p/prorata/
A quantitative proteomics software program for accurate protein abundance ratio estimation with confidence interval evaluation.
Proper citation: ProRata (RRID:SCR_002988) Copy
http://cakesomatic.sourceforge.net/
A bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone.
Proper citation: Cake (RRID:SCR_002133) Copy
http://www.bioconductor.org/packages/release/bioc/html/CAMERA.html
A Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data.
Proper citation: CAMERA - Collection of annotation related methods for mass spectrometry data (RRID:SCR_002466) Copy
http://cran.r-project.org/web/packages/isa2/
A biclustering algorithm that finds modules in an input matrix. A module or bicluster is a block of the reordered input matrix.
Proper citation: Iterative Signature Algorithm (RRID:SCR_002327) Copy
http://www.bioconductor.org/packages/release/bioc/html/iontree.html
Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry.
Proper citation: iontree (RRID:SCR_002813) Copy
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