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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
http://www.biostat.wisc.edu/~kendzior/EBSEQ/
Software R package for RNA-Seq Differential Expression Analysis.
Proper citation: EBSeq (RRID:SCR_003526) Copy
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
http://www.compgen.org/tools/metagen
Software program providing a method for meta-analysis of case-control genetic association studies using random-effects logistic regression.
Proper citation: metagen (RRID:SCR_003443) Copy
http://genome.sph.umich.edu/wiki/RAREMETAL
A software program that facilitates the meta-analysis of rare variants from genotype arrays or sequencing.
Proper citation: RAREMETAL (RRID:SCR_003573) Copy
http://erlichlab.wi.mit.edu/lobSTR/
A software tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: lobSTR (RRID:SCR_008030) Copy
http://bioinfo.cipf.es/isacghtrac
Software to analyze CNV that will now normalize arrays CGH and it will visually integrate different genome annotations.
Proper citation: IsaCGH (RRID:SCR_008375) Copy
http://mothra.ornl.gov/cgi-bin/cat/cat.cgi
A repository of tools for analysis and annotation of CAZYmes (Carbohydrate Active enZYmes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CAT (RRID:SCR_008421) Copy
http://bioinformatics.fccc.edu/software/OpenSource/FGDP/FGDP.shtml
A Java-based, Microarray or Genechip data analysis system.
Proper citation: FGDP (RRID:SCR_008910) Copy
http://www.labmedmolge.unisa.it/inglese/research/imir
A modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, DE analysis, target prediction by integrating multiple open source modules and resources in an automated workflow.
Proper citation: iMir (RRID:SCR_009496) Copy
http://www.stanford.edu/group/wonglab/SpliceMap/
A de novo splice junction discovery and alignment tool.
Proper citation: SpliceMap (RRID:SCR_009650) Copy
http://dna.engr.uconn.edu/?page_id=105
Software package that can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data.
Proper citation: IsoEM (RRID:SCR_009993) Copy
http://code.google.com/p/bitseq/
A software application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions.
Proper citation: BitSeq (RRID:SCR_009904) Copy
http://www.bioconductor.org/packages/2.13/bioc/html/cqn.html
A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method.
Proper citation: CQN (RRID:SCR_001786) Copy
http://www.bioconductor.org/packages/release/bioc/html/ADaCGH2.html
Software for analysis and plotting of array comparative genomic hybridization (CGH) data. It allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.
Proper citation: ADaCGH2 (RRID:SCR_001981) Copy
https://cran.r-project.org/src/contrib/Archive/PurBayes/
An MCMC-based algorithm that uses next-generation sequencing data to estimate tumor purity and clonality for paired tumor-normal data.
Proper citation: PurBayes (RRID:SCR_002068) Copy
https://github.com/BEETL/BEETL
Software tool that not only compresses FASTQ-formatted DNA reads more compactly than gzip but also permits rapid search for k-mer queries within the archived sequences. The full FASTQ record of each matching read or read pair is returned, allowing the search results to be piped directly to any of the many standard tools that accept FASTQ data as input. Searchable compressed archive for DNA reads.
Proper citation: BEETL-fastq (RRID:SCR_002341) Copy
http://www.ncbi.nlm.nih.gov/tools/gbench/
An integrated application for viewing and analyzing sequence data.
Proper citation: NCBI Genome Workbench (RRID:SCR_011794) Copy
https://code.google.com/p/ngsplot/
A software program that allows you to easily visualize your next-generation sequencing (NGS) samples at functional genomic regions.
Proper citation: ngs.plot (RRID:SCR_011795) Copy
http://www.cs.utah.edu/~miriah/mizbee/Overview.html
A multiscale synteny browser for exploring conservation relationships in comparative genomics data.
Proper citation: MizBee (RRID:SCR_011804) Copy
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