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

Software for fast and very memory-efficient calculation of isotope patterns, subsequent convolution to theoretical envelopes (profiles) plus valley detection and centroidization or intensoid calculation. Batch processing, resolution interpolation, wrapper, adduct calculations and molecular formula parsing.

Proper citation: enviPat (RRID:SCR_003034) Copy   

•   Source: SciCrunch Registry

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

Sequence analysis toolkit that contains a lot of sequence analysis algorithms, including methods for 1) motif statistics, e.g. compute the exact occurrence count distribution of a motif, 2) exact motif discovery: extraction of motifs with provably optimal p-value, 3) analysis of pattern matching algorithms: compute (for given algorithm and pattern) the exact distribution of the number of character accesses caused by searching a random text, 4) statistics of fragment masses resulting from proteolytic cleavage of proteins, 5) computing the expectated read length of sequencing reads for a given dispensation order (for 454 or IonTorrent) and 6) analysing sensitivity of spaced alignment seeds.

Proper citation: MoSDi (RRID:SCR_003037) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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

Software package for quantitative DNA sequencing for chromosomal aberrations providing a robust, cost-effective WGS method for DNA copy number analysis. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.

Proper citation: QDNAseq (RRID:SCR_003174) Copy   

•   Source: SciCrunch Registry

http://updepla1srv1.epfl.ch/waszaks/absfilter/

R package for identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.

Proper citation: ABS filter (RRID:SCR_005328) Copy   

•   Source: SciCrunch Registry

https://apsampler.sourceforge.net/

A software tool that allows multi-locus and multi-level association analysis of genotypic and phenotypic data.

Proper citation: APSampler (RRID:SCR_000042) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30, 2022. Software package that implements 12 major meta-analysis methods for differential expression analysis.Package was removed from the CRAN repository.Formerly available versions can be obtained from the archive.Archived on 2018-01-23 as check problems were not corrected in time.

Proper citation: MetaDE (RRID:SCR_000199) 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://cutenmr.sourceforge.net/

A multi-platform NMR processing application.

Proper citation: cuteNMR (RRID:SCR_000347) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/jmoldraw/

2-D chemical structure drawing software program.

Proper citation: JMolDraw (RRID:SCR_000349) 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://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://facil-host.cmbi.umcn.nl/facil

Genetic code prediction tool that infers the genetic code directly from any set of nucleic acid sequences and assigns a Random Forest-based reliability score to its predictions.

Proper citation: FACIL (RRID:SCR_004375) Copy   

•   Source: SciCrunch Registry

http://www.mathcs.emory.edu/panda/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Web-based software program for analyzing phosphorylation antibody arrays. It identifies phosphorylated antibodies in the microarray and statistically quantifies the extent of phosphorylation for these antibodies.

Proper citation: Phosphor Antibody Array Data Analysis (RRID:SCR_000633) Copy   

•   Source: SciCrunch Registry

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

A software package that provides functions to read raw RT-qPCR data of different platforms.

Proper citation: ReadqPCR (RRID:SCR_000030) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/heuraa/

Software for accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing.

Proper citation: HeurAA (RRID:SCR_013212) Copy   

•   Source: SciCrunch Registry

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

A software tool for high speed estimation of homology relations within and between species in massive data sets.

Proper citation: orthAgogue (RRID:SCR_011979) Copy   

•   Source: SciCrunch Registry

http://transcriptome.ens.fr/eoulsan/

A versatile framework based on the Hadoop implementation of the MapReduce algorithm, dedicated to high throughput sequencing data analysis on distributed computers.

Proper citation: Eoulsan (RRID:SCR_011901) Copy   

•   Source: SciCrunch Registry

http://qutemol.sourceforge.net/

Open source (GPL) software providing an interactive, high quality molecular visualization system.

Proper citation: QuteMol (RRID:SCR_012089) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/pride-converter-2/

Suite of software tools that allows users to convert search result files into PRIDE XML, generate mzTab skeleton files that can be used as a basis to submit quantitative and gel-based MS data, and post-process PRIDE XML files by filtering out contaminants and empty spectra.

Proper citation: PRIDE Converter 2 (RRID:SCR_012051) Copy   

•   Source: SciCrunch Registry