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http://taylorlab.ucsf.edu/software_data.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documentedt on January 10, 2023. Software that implements babel routines for identifying unusual ribosome protected fragment counts given mRNA counts, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Babel (RRID:SCR_004307) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/QuickGO/

A web-based browser for Gene Ontology terms and annotations, which is provided by the UniProtKB-GOA group at the EBI. It is able to offer a range of facilities including bulk downloads of GO annotation data which can be extensively filtered by a range of different parameters and GO slim set generation. The software for QuickGO is freely available under the Apache 2 license. QuickGO can supply GO term information and GO annotation data via REST web services.

Proper citation: QuickGO (RRID:SCR_004608) Copy   

•   Source: SciCrunch Registry

http://www.omicsoft.com/fusionmap/

An efficient fusion aligner which aligns reads spanning fusion junctions directly to the genome without prior knowledge of potential fusion regions. It detects and characterizes fusion junctions at base-pair resolution. FusionMap can be applied to detect fusion junctions in both single- and paired-end dataset from either gDNA-Seq or RNA-Seq studies. FusionMap runs under both Windows and Linux (requiring MONO) environments. Although it can run on 32 bit machine, it is recommended to run on 64-bit machine with 8GB RAM or more. If you have an ArrayStudio License, you can run the fusion detection easily through its GUI.

Proper citation: FusionMap (RRID:SCR_005242) Copy   

•   Source: SciCrunch Registry

http://www.bsse.ethz.ch/cbg/software/shorah

A software package that allows for inference about the structure of a population from a set of short sequence reads as obtained from ultra-deep sequencing of a mixed sample. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.

Proper citation: ShoRAH (RRID:SCR_005211) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/devel/bioc/html/DMRforPairs.html

Software for identifying differentially methylated regions between unique samples using array based methylation profiles. It allows researchers to compare n greater than or equal to 2 unique samples with regard to their methylation profile. The (pairwise) comparison of n unique single samples distinguishesit from other existing pipelines as these often compare groups of samples in either single CpG locus or region based analysis. DMRforPairs defines regions of interest as genomic ranges with sufficient probes located in close proximity to each other. Probes in one region are optionally annotated to the same functional class(es). Differential methylation is evaluated by comparing the methylation values within each region between individual samples and (if the difference is sufficiently large), testing this difference formally for statistical significance.

Proper citation: DMRforPairs (RRID:SCR_005702) Copy   

•   Source: SciCrunch Registry

http://llama.mshri.on.ca/gofish/GoFishWelcome.html

Software program, available as a Java applet online or to download, allows the user to select a subset of Gene Ontology (GO) attributes, and ranks genes according to the probability of having all those attributes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GoFish (RRID:SCR_005682) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for modeling count data using Dirichlet-multinomial and beta-binomial mixtures with applications to single-cell assays.

Proper citation: MIMOSA (RRID:SCR_000184) Copy   

•   Source: SciCrunch Registry

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

Software that uses a Bayesian hierarchical mixture model to learn correlation patterns of allele-specificity among multiple proteins.

Proper citation: iASeq (RRID:SCR_000420) Copy   

•   Source: SciCrunch Registry

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

An R/Bioconductor package that interfaces the X!Tandem protein identification algorithm.

Proper citation: rTANDEM (RRID:SCR_000409) Copy   

•   Source: SciCrunch Registry

https://github.com/yongchao/flowPeaks

Software for fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.

Proper citation: flowPeaks (RRID:SCR_000407) Copy   

•   Source: SciCrunch Registry

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

Software that provides quality control and quality assessment tools for gated flow cytometry data.

Proper citation: QUALIFIER (RRID:SCR_000389) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/src/contrib/Archive/sybil/

A Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis). This is an implementation of COBRA toolbox in R language.

Proper citation: sybil - Efficient Constrained Based Modelling in R (RRID:SCR_000457) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/Rdisop.html

Software for identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists.

Proper citation: Rdisop (RRID:SCR_000453) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/flipflop.html

Software that discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data.

Proper citation: FlipFlop (RRID:SCR_000625) Copy   

•   Source: SciCrunch Registry

http://www.filemaker.com

A database software for managing, analyzing and sharing information across multiple devices and people, both online and offline.

Proper citation: FileMaker (RRID:SCR_000783) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/dkessner/forqs

Software for forward-in-time population genetics simulation that tracks individual haplotype chunks as they recombine each generation. It also also models quantitative traits and selection on those traits.

Proper citation: forqs (RRID:SCR_000643) Copy   

•   Source: SciCrunch Registry

http://www.psb.ugent.be/esb/PiNGO/

A Java-based tool to easily find unknown genes in a network that are significantly associated with user-defined target Gene Ontology (GO) categories. PiNGO is implemented as a plugin for Cytoscape, a popular open source software platform for visualizing and integrating molecular interaction networks. PiNGO predicts the categorization of a gene based on the annotations of its neighbors, using the enrichment statistics of its sister tool BiNGO. Networks can either be selected from the Cytoscape interface or uploaded from file. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: PiNGO (RRID:SCR_000692) Copy   

•   Source: SciCrunch Registry

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

A Java application programming interface (API) for the Proteomics Standards Initiative mzML data standard.

Proper citation: jmzML (RRID:SCR_001119) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/devel/bioc/html/massiR.html

Software that predicts the sex of samples in gene expression microarray datasets.

Proper citation: massiR (RRID:SCR_001157) Copy   

•   Source: SciCrunch Registry

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

Software R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.

Proper citation: DSS (RRID:SCR_002754) Copy   

•   Source: SciCrunch Registry