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http://sourceforge.net/projects/as-peak/

A software that utilizes a peak detection algorithm to identify RNA-protein binding sites.

Proper citation: AS-Peak (RRID:SCR_000380) Copy   

•   Source: SciCrunch Registry

http://cellnet.cecad.uni-koeln.de/15763.html

R software package for transcription factor (TF) target gene prediction based on ChIP-seq data. Version 0.4 contains code to compute FDR-corrected q-values via permutations of the peak-to-gene assignments (ClosestGene only).

Proper citation: TargetCaller (RRID:SCR_000414) Copy   

•   Source: SciCrunch Registry

http://www.bzip.org/

A data compressor for files. This software is freely available, patent free, and is organized as a library with a programming interface.

Proper citation: bzip2 (RRID:SCR_000376) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowFlowJo.html

A Bioconductor package that can import gates defined by the commercial package FlowJo and work with them in a manner consistent with the other flow packages in Bioconductor. FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the FlowJo Workspace. This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm.

Proper citation: flowFlowJo (RRID:SCR_000410) Copy   

•   Source: SciCrunch Registry

http://open2dprot.sourceforge.net/Flicker/

An open-source stand-alone computer program for visually comparing 2D gel images.

Proper citation: Flicker (RRID:SCR_000288) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/omssapercolator/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software tool which interfaces OMSSA with Percolator, a post search machine learning method for rescoring database search results.

Proper citation: OMSSAPercolator (RRID:SCR_000287) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/OLINgui.html

Software package providing a graphical user interface for the OLIN package.

Proper citation: OLINgui (RRID:SCR_000435) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/arrayplex/

Open source software that integrates various forms of microarray data from diverse annotation and primary data sources. This software provides a programmatic framework (API set) that will be used for collaborative development and deploys an easy to maintain client-server architecture.

Proper citation: ArrayPlex (RRID:SCR_000312) Copy   

•   Source: SciCrunch Registry

http://life.tongji.edu.cn/meqa/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2022. Software for pre-processing, quality assessment, read distribution and methylation estimation for MeDIP-sequence datasets. It has the ability to quickly analyze sequence data for DNA methylation. This software integrates customized scripting and existing utilities tools that work on both paired end and single end data.

Proper citation: MeQA (RRID:SCR_000317) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/microanalyzer/

Java tool that performs the preprocessing of Expression and SNPs microarray Affymetrix. The software allows the automatic download and the use of the clustering and visualization software as the Mev 4.0. The tool is equipped by a graphical interface (Swing) that allows to the user to: Create the workspace (files .cel, preferred algorithms , output, libraries to use); Run/save analysis and workspace settings (xml); Efficient download of the libraries (http, ftp, MD5); Customize basic and graphical settings (objects serialization and deserialization). Type of SNPs: Mapping 500k or preceding chips, SNP 5.0, SNP 6.0. Available for 32 or 64 bit systems, and for Windows and Linux Systems.

Proper citation: Micro-Analyzer (RRID:SCR_000394) Copy   

•   Source: SciCrunch Registry

http://functsnp.sourceforge.net/

An R package for linking SNPs (Single Nucleotide Polymorphisms) to functional knowledge.

Proper citation: FunctSNP (RRID:SCR_000393) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowStats.html

Software using statistical methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the flowCore package.

Proper citation: flowStats (RRID:SCR_000399) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/d2-tools/

Software toolbox for counting the frequency of K-tuple from sequencing datasets and calculate the dissimilarity.

Proper citation: d2-tools (RRID:SCR_000425) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/2.12/bioc/html/Clonality.html

Software package for clonality testing providing statistical tests for clonality versus independence of tumors from the same patient based on their loss of heterozygosity (LOH) or genomewide copy number profiles.

Proper citation: Clonality (RRID:SCR_000293) Copy   

•   Source: SciCrunch Registry

https://github.com/johnomics/RADtools

Software tools for processing RAD Sequencing Illumina reads. Version 1.0 is a pipeline for transforming Illumina reads into candidate genetic markers.

Proper citation: RADtools (RRID:SCR_000324) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/emesbioinformatics/group-software/nimbl

MATLAB code to quality control and prioritize differentially methylated markers from illumina infinium arrays.

Proper citation: NIMBL (RRID:SCR_000482) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/iBMQ.html

Software for integrated Bayesian Modeling of eQTL data. It implements a joint hierarchical Bayesian model where all genes and SNPs are modeled concurrently.

Proper citation: iBMQ (RRID:SCR_000481) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/foursig/

A suite of software programs for analyzing and visualizing 4C-seq data.

Proper citation: fourSig (RRID:SCR_000516) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.tapyr.net/

An efficient software tool for the local alignment of pyrosequencing reads produced by the GS FLX (454) Genome Analyzer technology against a reference genome sequence. The approach explores the characteristics of the data in re-sequencing applications and uses state of the art BWT-based indexing techniques combined with a flexible seed-based approach, leading to a fast and accurate algorithm which needs very little user parameterization. Although initially developed having this specific technology in mind, this software performs equally well on any other platform that can return its sequencing reads in the FASTA, FASTQ or SFF formats, including Illumina, Ion Torrent and Pacific Biosciences technologies.

Proper citation: TAPyR (RRID:SCR_000588) Copy   

•   Source: SciCrunch Registry