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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
  

https://www.ebi.ac.uk/jdispatcher/msa/clustalo?stype=protein

Software package as multiple sequence alignment tool that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. Accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/Clustal, GCG/MSF, RSF.

Proper citation: Clustal Omega (RRID:SCR_001591) 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://soap.genomics.org.cn/SOAPfusion.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 22,2022. An open source software tool for fusion discovery with paired-end RNA-Seq reads. The tool follows a different strategy by finding fusions directly and verifying them, differentiating it from all other existing tools by finding the candidate regions and searching for the fusions afterwards.

Proper citation: SOAPfusion (RRID:SCR_000079) Copy   

•   Source: SciCrunch Registry
  

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

Software functions for data analysis and graphical displays for developmental microarray time course data.

Proper citation: timecourse (RRID:SCR_000077) Copy   

•   Source: SciCrunch Registry
  

http://patchwork.r-forge.r-project.org/

Software tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid. Patchwork takes BAM files as input whereas PatchworkCG takes input from CompleteGenomics files. TAPS performs the same analysis as Patchwork but for microarray data.

Proper citation: Patchwork (RRID:SCR_000072) 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
  

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

Desktop application for analysis and visualization of large-scale cell signaling networks.

Proper citation: SNAVI (RRID:SCR_000091) 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://cistrome.org

Web based integrative platform for transcriptional regulation studies.

Proper citation: Cistrome (RRID:SCR_000242) 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://www.bioconductor.org/packages/release/bioc/html/AffyRNADegradation.html

Software package that helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.

Proper citation: AffyRNADegradation (RRID:SCR_000118) 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://docking.sce.ntu.edu.sg/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Web service that is used by researchers and scientists to perform protein-ligand covalent docking. This form allows for the formation of covalent linkages between the ligand and the receptor.

Proper citation: CovalentDock Cloud (RRID:SCR_000126) 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://www.bioconductor.org/packages/release/bioc/html/cn.farms.html

Software R package for copy number variation analysis that allows analysis of the most common Affymetrix (250K-SNP6.0) array types and supports high-performance computing using snow and ff.

Proper citation: cn.FARMS (RRID:SCR_000289) 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