Tools   Select Another Resource Report Type

http://bioinfo2.ugr.es/MethylExtract/

A user friendly software tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation.

Proper citation: MethylExtract (RRID:SCR_005446) Copy   

•   Source: SciCrunch Registry

http://campagnelab.org/software/gobyweb/

Web application that facilitates the management and analysis of high-throughput sequencing (HTS) data. In the back-end, it uses the Goby framework, BWA, STAR, Last, GSNAP, Samtools, VCF-tools, along with a cluster of servers to provide rapid alignment and efficient analyses. GobyWeb makes it possible to analyze hundreds of samples in consistent ways without having to use command line tools. GobyWeb provides tools that streamline frequent data analyses for RNA-Seq, Methyl-Seq, RRBS, or DNA-Seq datasets and to enable teams of investigators to share reads and results of analyses. GobyWeb can be extended for new analyses by developing plugins.

Proper citation: GobyWeb (RRID:SCR_005443) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/p/treq/home/Home/

A software read mapper for high-throughput DNA sequencing reads, in particular one to several hundred nucleotides in length, and for large edit distance between sequencing read and match in the reference genome. It can cope particularly well with indels for single-best hit recall of 200nt reads simulated from the human reference genome. TreQ performs best at a running time comparable to BWA at large edit distance settings.

Proper citation: TreQ (RRID:SCR_005505) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://pymzml.github.io/

Python module to parse mzML data in Python based on cElementTree. It is an extension to Python that offers (i) an easy access to mass spectrometry (MS) data that allows the rapid development of tools, (ii) a very fast parser for mzML data and (iii) a set of functions to compare or handle spectra., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: pymzML (RRID:SCR_002500) Copy   

•   Source: SciCrunch Registry

http://bioinfo3d.cs.tau.ac.il/FlexProt/

FlexProt detects the optimal flexible structural alignment of a pair of protein structures. The first structure is assumed to be rigid, while in the second structure potential flexible regions are automatically detected.

Proper citation: FlexProt: flexible protein alignment (RRID:SCR_007306) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/taipan/

A fast hybrid short-read assembly tool.

Proper citation: Taipan (RRID:SCR_007330) Copy   

•   Source: SciCrunch Registry

http://genotan.sourceforge.net/

A free software tool to identify length variation of microsatellites from short sequence reads.

Proper citation: GenoTan (RRID:SCR_007935) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/huber-srv/hilbert/

Software tool that allows to display very long data vectors in a space-efficient manner, allowing the user to visually judge the large scale structure and distribution of features simultaneously with the rough shape and intensity of individual features.

Proper citation: HilbertVis (RRID:SCR_007862) Copy   

•   Source: SciCrunch Registry

http://brig.sourceforge.net/

A cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.

Proper citation: BRIG (RRID:SCR_007802) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.stanford.edu/group/wonglab/SpliceMap/

A de novo splice junction discovery and alignment tool.

Proper citation: SpliceMap (RRID:SCR_009650) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry