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http://www.scfbio-iitd.res.in/sanjeevini/sanjeevini.jsp

A complete drug designing software suite with an accessible web-server for targeted directed lead molecule discovery.

Proper citation: Sanjeevini (RRID:SCR_000191) Copy   

•   Source: SciCrunch Registry
  

http://exon.gatech.edu/paul/unsplicer/index.htm

An RNA-seq alignment program that provides alignment of short reads to a reference genome. The program requires two inputs that are provided by the output of GeneMark-ES: HMM model parameters and ab initio gene predictions. UnSplicer is a sister pipeline to TrueSight.

Proper citation: UnSplicer (RRID:SCR_000226) Copy   

•   Source: SciCrunch Registry
  

https://github.com/matteocereda/RNAmotifs

Software that evaluates the sequence around differentially regulated alternative exons to identify clusters of short and degenerate sequences, referred to as multivalent RNA motifs.

Proper citation: RNAmotifs (RRID:SCR_000263) 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://bioinfo5.ugr.es/miRanalyzer/miRanalyzer.php

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. A microRNA detection and analysis tool for next-generation sequencing experiments. The program uses a minimum match length of 17bp starting at the first base of the read. The maximum read length is set to 28bp. Reads with more than 5 matches to the genome are discarded, and if a read matches to more than 5 transcripts or Rfam entries it will be removed.

Proper citation: miRanalyzer (RRID:SCR_000163) Copy   

•   Source: SciCrunch Registry
  

http://www.dnastar.com/t-seqmanpro.aspx

Software for analysis and DNA sequence assembly of Sanger data. It also provides visualizations and analysis of next-gen projects assembled by SeqMan NGen.

Proper citation: Lasergene's SeqMan Pro (RRID:SCR_000283) 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://sourceforge.net/projects/biogrinder/

An open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms. The tool is available through multiple interfaces like GUI, CLI and API. It is useful for simulating clinical or environmental microbial communities and complements the use of in vitro mock communities.

Proper citation: Grinder (RRID:SCR_000168) 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://sourceforge.net/projects/omssapercolator/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software tool which interfaces OMSSA with Percolator, a post search machine learning method for rescoring database search results.

Proper citation: OMSSAPercolator (RRID:SCR_000287) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/devel/bioc/html/CNTools.html

Software package that provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data.

Proper citation: CNTools (RRID:SCR_000281) Copy   

•   Source: SciCrunch Registry
  

http://gprox.sourceforge.net/

A freely available complete software platform for comprehensive and integrated analysis and visualization of large proteomics datasets.

Proper citation: GProX (RRID:SCR_000273) 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.mmnt.net/db/0/0/ftp-genome.wi.mit.edu/distribution/GISTIC2.0

Software to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth. By separating SCNA profiles into underlying arm-level and focal alterations, they improve the estimation of background rates for each category.

Proper citation: GISTIC (RRID:SCR_000151) Copy   

•   Source: SciCrunch Registry
  

http://www.cs.utexas.edu/~bajaj/cvc/software/f2dockclient.shtml

A collection of user interfaces packaged into TexMol that allows a user to interactively submit protein-protein docking jobs to a remote computing cluster, monitor the status of the jobs and retrieve and visually display/compare the results.

Proper citation: F2DockClient (RRID:SCR_000185) Copy   

•   Source: SciCrunch Registry
  

http://www.biosolveit.de/flexx/index.html?ct=1

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software with two main applications: predicting the binding mode of three-dimensional proteins and virtual high-throughput screening (vHTS) which allows screening of compounds at rapid speeds.

Proper citation: FlexX (RRID:SCR_000186) Copy   

•   Source: SciCrunch Registry
  

http://www.cs.toronto.edu/~hilal/rnacontext/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Motif finding software suited for using large-scale RNA-binding affinity datasets to determine the relative binding preferences of RNA-binding proteins (RBPs) for a wide range of RNA sequences and structures. The tool is also implemented in a website.

Proper citation: RNAcontext (RRID:SCR_000179) Copy   

•   Source: SciCrunch Registry
  

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

Software package that quantifies the similarity of cell populations across multiple flow cytometry samples using a nonparametric multivariate statistical test. The algorithm allows the users to specify a reference sample for comparison or to construct a reference sample from the available data. The output of the algorithm is a set of text files where the cell population labels are replaced by a metaset of population labels, generated from the matching process.

Proper citation: flowMap (RRID:SCR_002269) Copy   

•   Source: SciCrunch Registry
  

http://cakesomatic.sourceforge.net/

A bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone.

Proper citation: Cake (RRID:SCR_002133) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/matchprot/

A pairwise protein structure alignment software.

Proper citation: Matchprot (RRID:SCR_002163) Copy   

•   Source: SciCrunch Registry