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http://minia.genouest.org/dsk/

A k-mer counting software that can count k-mers of large Illumina datasets on laptops and desktop computers.

Proper citation: DSK (RRID:SCR_001246) Copy   

•   Source: SciCrunch Registry

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

Software package for Illumina 450 methylation array normalization and metrics including 15 flavors of betas and three performance metrics, with methods for objects produced by methylumi, minfi and IMA packages.

Proper citation: wateRmelon (RRID:SCR_001296) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ngsrich/

Software for target enrichment performance for next-generation sequencing.

Proper citation: NGSrich (RRID:SCR_001333) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.10/bioc/html/oneChannelGUI.html

Software library that provides a graphical interface for microarray gene and exon level analysis as well as miRNA/mRNA-seq data analysis. The package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code.

Proper citation: oneChannelGUI (RRID:SCR_001325) Copy   

•   Source: SciCrunch Registry

http://itb.biologie.hu-berlin.de/~futschik/software/R/cycle/index.html

Software package for the identification of periodically expressed genes using Fourier analysis and the statistical assessment of significance using different background models.

Proper citation: CYCLE (RRID:SCR_001328) Copy   

•   Source: SciCrunch Registry

http://bioinf.wehi.edu.au/affylmGUI/

R software package providing a Graphical User Interface for analysis of Affymetrix microarray data, using the limma package (Linear Models for MicroArray data). While not as powerful as limma to the expert user, it offers a simple point-and-click interface to many of the commonly-used limma and affy functions. You need to have R 1.9.0 or later, Tcl/Tk 8.3 or later (ActiveTcl for Windows, Tcl/Tk Source for Linux/Unix, or X11 Tcl/Tk for MacOSX) and the limma, affylmGUI, and tkrplot R packages. It has been succesfully tested on Windows 2000, Windows XP, RedHat/Fedora Linux, and on Mac OSX with X11.

Proper citation: affylmGUI (RRID:SCR_001320) Copy   

•   Source: SciCrunch Registry

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

Software to detect differential expression in microarray and proteomics datasets. Its use has been shown to improve the detection of differentially expressed genes or proteins in these datasets.

Proper citation: plgem (RRID:SCR_001355) Copy   

•   Source: SciCrunch Registry

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

Preprocessing and analysis software for single microarrays and microarray batches.

Proper citation: fRMA (RRID:SCR_001345) Copy   

•   Source: SciCrunch Registry

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

Software package using the GASSCO method for correcting for slide-dependent gene-specific dye bias.

Proper citation: dyebias (RRID:SCR_001308) Copy   

•   Source: SciCrunch Registry

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

Software package for a Graphical User Interface for the limma Microarray package.

Proper citation: limmaGUI (RRID:SCR_001306) Copy   

•   Source: SciCrunch Registry

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

Software to identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).

Proper citation: ffpe (RRID:SCR_001307) Copy   

•   Source: SciCrunch Registry

http://microbiology.se/software/megraft/

A software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes.

Proper citation: Megraft (RRID:SCR_000240) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.utoronto.ca/varid/

Software using a Hidden Markov Model for SNP (single nucleotide polymorphism) and indel identification with AB-SOLiD color-space as well as regular letter-space reads.

Proper citation: VARiD (RRID:SCR_000241) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.psb.ugent.be/webtools/tapir/

Web server designed for prediction of plant microRNA targets.

Proper citation: TAPIR: target prediction for plant microRNAs (RRID:SCR_000237) Copy   

•   Source: SciCrunch Registry

http://iclab.life.nctu.edu.tw/iclab_webtools/sodock/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An optimization algorithm based on particle swarm optimization (PSO) for solving flexible protein-ligand docking problems.

Proper citation: SODOCK (RRID:SCR_000193) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/protms/

A software tool for the proteomics community that may help improving analysis of proteomic experimental data.

Proper citation: Quant (RRID:SCR_000267) Copy   

•   Source: SciCrunch Registry

http://peptideprophet.sourceforge.net/

Software that automatically validates peptide assignments to MS/MS spectra made by database search programs such as SEQUEST.

Proper citation: PeptideProphet (RRID:SCR_000274) Copy   

•   Source: SciCrunch Registry

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

Software package that contains the function for filtering genes by the proportion of variation accounted for by the first principal component (PVAC).

Proper citation: pvac (RRID:SCR_000359) 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://life.tongji.edu.cn/meqa/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2022. Software for pre-processing, quality assessment, read distribution and methylation estimation for MeDIP-sequence datasets. It has the ability to quickly analyze sequence data for DNA methylation. This software integrates customized scripting and existing utilities tools that work on both paired end and single end data.

Proper citation: MeQA (RRID:SCR_000317) Copy   

•   Source: SciCrunch Registry