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http://www.bioinf.uni-freiburg.de/Software/GraphProt/

Software for modeling binding preferences of RNA-binding proteins from high-throughput experiments such as CLIP-seq and RNAcompete.

Proper citation: GraphProt (RRID:SCR_005842) Copy   

•   Source: SciCrunch Registry

http://www-math.u-strasbg.fr/genpred/spip.php?article3

R software package to study, predict and simulate the diffusion of a signal through a temporal gene network. It predicts changes in gene expressions after a biological perturbation in the network and provides graphical outputs that allow monitoring the spread of a signal through the network., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Cascade (RRID:SCR_005861) Copy   

•   Source: SciCrunch Registry

http://www.psb.ugent.be/cbd/papers/BiNGO/Home.html

The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java tool to determine which Gene Ontology (GO) terms are significantly overrepresented in a set of genes. BiNGO can be used either on a list of genes, pasted as text, or interactively on subgraphs of biological networks visualized in Cytoscape. BiNGO maps the predominant functional themes of the tested gene set on the GO hierarchy, and takes advantage of Cytoscape''''s versatile visualization environment to produce an intuitive and customizable visual representation of the results. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: BiNGO: A Biological Networks Gene Ontology tool (RRID:SCR_005736) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.14/bioc/html/h5vc.html

Software package that contains functions to interact with tally data from Next-Generation Sequencing (NGS) experiments that is stored in HDF5 files.

Proper citation: h5vc (RRID:SCR_006039) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/IRanges/

Software tool for computing and annotating genomic ranges.Provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as Vector objects), as well as views on these Vector objects. Efficient list-like classes are also provided for storing big collections of instances of the basic classes. All classes in the package use consistent naming and share the same rich and consistent Vector API as much as possible.

Proper citation: IRanges (RRID:SCR_006420) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/vicuna

A de novo assembly program targeting populations with high mutation rates.

Proper citation: VICUNA (RRID:SCR_006302) Copy   

•   Source: SciCrunch Registry

https://github.com/ding-lab/msisensor

A C++ software program for automatically detecting somatic and germline variants at microsatellite regions. It computes length distributions of microsatellites per site in paired tumor and normal sequence data, subsequently using these to statistically compare observed distributions in both samples.

Proper citation: MSIsensor (RRID:SCR_006418) Copy   

•   Source: SciCrunch Registry

http://www.clipz.unibas.ch/downloads/TSSer/index.php

A computational pipeline to analyze differential RNA sequencing (dRNA-seq) data to determine transcription start sites genome-wide.

Proper citation: TSSer (RRID:SCR_006419) Copy   

•   Source: SciCrunch Registry

http://gepat.sourceforge.net/

A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context.

Proper citation: GEPAT (RRID:SCR_003597) Copy   

•   Source: SciCrunch Registry

http://jexpress.bioinfo.no/site/

Gene expression analysis software using Java.

Proper citation: J-Express (RRID:SCR_003609) Copy   

•   Source: SciCrunch Registry

http://mendel.stanford.edu/sidowlab/downloads/quest/

A Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitation (ChIP-seq) experiments.

Proper citation: Quantitative Enrichment of Sequence Tags (RRID:SCR_004065) Copy   

•   Source: SciCrunch Registry

http://www.brl.bcm.tmc.edu/pash/pashDownload.rhtml

Performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite sequencing.

Proper citation: Pash 3.0 (RRID:SCR_004078) Copy   

•   Source: SciCrunch Registry

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

Software package that helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.

Proper citation: AffyRNADegradation (RRID:SCR_000118) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 22,2022. An open source software tool for fusion discovery with paired-end RNA-Seq reads. The tool follows a different strategy by finding fusions directly and verifying them, differentiating it from all other existing tools by finding the candidate regions and searching for the fusions afterwards.

Proper citation: SOAPfusion (RRID:SCR_000079) Copy   

•   Source: SciCrunch Registry

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

Software functions for data analysis and graphical displays for developmental microarray time course data.

Proper citation: timecourse (RRID:SCR_000077) Copy   

•   Source: SciCrunch Registry

http://patchwork.r-forge.r-project.org/

Software tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid. Patchwork takes BAM files as input whereas PatchworkCG takes input from CompleteGenomics files. TAPS performs the same analysis as Patchwork but for microarray data.

Proper citation: Patchwork (RRID:SCR_000072) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://microbiology.se/software/megraft/

A software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes.

Proper citation: Megraft (RRID:SCR_000240) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.utoronto.ca/varid/

Software using a Hidden Markov Model for SNP (single nucleotide polymorphism) and indel identification with AB-SOLiD color-space as well as regular letter-space reads.

Proper citation: VARiD (RRID:SCR_000241) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.psb.ugent.be/webtools/tapir/

Web server designed for prediction of plant microRNA targets.

Proper citation: TAPIR: target prediction for plant microRNAs (RRID:SCR_000237) Copy   

•   Source: SciCrunch Registry