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https://code.google.com/p/popoolation2/

Software to compare allele frequencies for SNPs between two or more populations and to identify significant differences. PoPoolation2 requires next generation sequencing data of pooled genomic DNA (Pool-Seq). It may be used for measuring differentiation between populations, for genome wide association studies and for experimental evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PoPoolation2 (RRID:SCR_003284) Copy   

•   Source: SciCrunch Registry

https://github.com/outbig/DAFGA

A python script package which estimates the evolutionary rate of a particular functional gene in a standardized manner by relating its sequence divergence to that of the 16S rRNA gene. It provides gene-specific parameter sets for OTU clustering and taxonomic assignment at desired rank, and it can be implemented into the diversity measurements offered by QIIME or Mothur.

Proper citation: DAFGA (RRID:SCR_003319) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/johanneskoester/snakemake/wiki/

A Python based language and execution environment for make-like workflows. The system supports the use of automatically inferred multiple named wildcards (or variables) in input and output filenames.

Proper citation: Snakemake (RRID:SCR_003475) Copy   

•   Source: SciCrunch Registry

http://knowledgemap.mc.vanderbilt.edu/research/content/phewas-r-package

Software package contains methods for performing Phenome-Wide Association Study.

Proper citation: PheWAS R Package (RRID:SCR_003512) Copy   

•   Source: SciCrunch Registry

https://github.com/BauerLab/ngsane

Software providing a Linux-based High Performance Computing (HPC) enabled framework for high-throughput data analysis that minimizes overhead for set up and processing of new projects yet maintains full flexibility of custom scripting when processing raw sequence data.

Proper citation: NGSANE (RRID:SCR_003478) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/snape-pooled/

Software that computes the probability distribution for the frequency of the minor allele in a certain population, at a certain position in the genome.

Proper citation: SNAPE-pooled (RRID:SCR_003476) Copy   

•   Source: SciCrunch Registry

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

Software tool for running and managing bioinformatics pipelines. It specializes in enabling users to turn existing pipelines based on shell scripts or command line tools into highly flexible, adaptable and maintainable workflows with a minimum of effort. Bpipe ensures that pipelines execute in a controlled and repeatable fashion and keeps audit trails and logs to ensure that experimental results are reproducible. Requiring only Java as a dependency, it is fully self-contained and cross-platform, making it very easy to adopt and deploy into existing environments.

Proper citation: Bpipe (RRID:SCR_003471) Copy   

•   Source: SciCrunch Registry

http://www.lgm.upmc.fr/parseq/

Statistical software for transcription landscape reconstruction at a basepair resolution from RNA Seq read counts. It is based on a state-space model which describes, in terms of abrupt shifts and more progressive drifts, the transcription level dynamics along the genome. Alongside variations of transcription level, it incorporates a component of short-range variation to pull apart local artifacts causing correlated dispersion. Reconstruction of the transcription level relies on a conditional sequential Monte Carlo approach that is combined with parameter estimation in a Markov chain Monte Carlo algorithm known as particle Gibbs. The method allows to estimate the local transcription level, to call transcribed regions, and to identify the transcript borders.

Proper citation: Parseq (RRID:SCR_003464) Copy   

•   Source: SciCrunch Registry

http://ctrad-csi.nus.edu.sg/gbsa/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. Software for analyzing whole-genome bisulfite sequencing data.

Proper citation: GBSA (RRID:SCR_003413) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/MultiPhen/

Software package that performs genetic association tests between SNPs (one-at-a-time) and multiple phenotypes (separately or in joint model).

Proper citation: MultiPhen (RRID:SCR_003498) Copy   

•   Source: SciCrunch Registry

http://www.biostat.wisc.edu/~kendzior/EBSEQ/

Software R package for RNA-Seq Differential Expression Analysis.

Proper citation: EBSeq (RRID:SCR_003526) Copy   

•   Source: SciCrunch Registry

http://www.hsph.harvard.edu/skat/metaskat/

A R package for multiple marker meta-analysis.

Proper citation: MetaSKAT (RRID:SCR_003489) Copy   

•   Source: SciCrunch Registry

http://genomesavant.com/p/home/index

Next-generation genome browser software designed for the latest generation of genome data.

Proper citation: Savant (RRID:SCR_003488) Copy   

•   Source: SciCrunch Registry

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

A Java interface to the mzTab data exchange format for reporting a summary of proteomics results.

Proper citation: jmzTab (RRID:SCR_003481) Copy   

•   Source: SciCrunch Registry

https://www.leica-microsystems.com/products/confocal-microscopes/p/leica-tcs-spe/

High resolution, compact and robust confocal that enables immunohistochemical colocalization analysis of florescent markers. Leica TCS SPE confocal point-scanning, spectral system for fluorescence imaging of live or fixed cells.

Proper citation: Leica TCS SPE (RRID:SCR_002140) Copy   

•   Source: SciCrunch Registry

https://github.com/TGAC/miso-lims

Open source software for a Laboratory Information Management System (LIMS) for NGS sequencing centres.

Proper citation: miso-lims (RRID:SCR_002259) Copy   

•   Source: SciCrunch Registry

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

A Bioconductor package designed to perform quantitative analysis of cell proliferation in tracking dye-based experiments. The package uses an R implementation of the Levenberg-Marquardt algorithm (minpack.lm) to fit a set of peaks (corresponding to different generations of cells) over the proliferation-tracking dye distribution in a FACS experiment.

Proper citation: flowFit (RRID:SCR_002286) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.13/bioc/html/spliceR.html

An easy-to-use R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.

Proper citation: spliceR (RRID:SCR_002280) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/neuRosim/

Software package that allows users to generate fMRI time series or 4D data. Some high-level functions are created for fast data generation with only a few arguments and a diversity of functions to define activation and noise. For more advanced users it is possible to use the low-level functions and manipulate the arguments.

Proper citation: neuRosim (RRID:SCR_002154) Copy   

•   Source: SciCrunch Registry

https://www.bd.com/resource.aspx?IDX=17868

Benchtop high-performance cell sorter with multiple lazer, detector and fluoroscrome options. Allows detection of 12 parameters (10 color conjugates, forward and sideward scatter).

Proper citation: BD LSR II Flow Cytometer (RRID:SCR_002159) Copy   

•   Source: SciCrunch Registry