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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Alignment software for large-scale protein contact or protein-protein interaction prediction optimized for speed through shorter runtimes. FreeContact provides the opportunity to compute contact predictions in any environment (desktop or cloud).
Proper citation: FreeContact (RRID:SCR_016113) Copy
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
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
Web based integrative platform for transcriptional regulation studies.
Proper citation: Cistrome (RRID:SCR_000242) Copy
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
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
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
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
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
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
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
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
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
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
http://sourceforge.net/projects/microanalyzer/
Java tool that performs the preprocessing of Expression and SNPs microarray Affymetrix. The software allows the automatic download and the use of the clustering and visualization software as the Mev 4.0. The tool is equipped by a graphical interface (Swing) that allows to the user to: Create the workspace (files .cel, preferred algorithms , output, libraries to use); Run/save analysis and workspace settings (xml); Efficient download of the libraries (http, ftp, MD5); Customize basic and graphical settings (objects serialization and deserialization). Type of SNPs: Mapping 500k or preceding chips, SNP 5.0, SNP 6.0. Available for 32 or 64 bit systems, and for Windows and Linux Systems.
Proper citation: Micro-Analyzer (RRID:SCR_000394) Copy
A user-sponsored molecular visualization software system on an open-source foundation. The software has the capabilities to view, render, animate, export, present and develop three dimensional molecular structures.
Proper citation: PyMOL (RRID:SCR_000305) Copy
https://github.com/GregoryFaust/samblaster
Software tool to mark duplicates and extract discordant and split reads from SAM files. This fast and flexible program for marking duplicates in read-id grouped paired-end SAM files can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.
Proper citation: SAMBLASTER (RRID:SCR_000468) Copy
An efficient software tool for the local alignment of pyrosequencing reads produced by the GS FLX (454) Genome Analyzer technology against a reference genome sequence. The approach explores the characteristics of the data in re-sequencing applications and uses state of the art BWT-based indexing techniques combined with a flexible seed-based approach, leading to a fast and accurate algorithm which needs very little user parameterization. Although initially developed having this specific technology in mind, this software performs equally well on any other platform that can return its sequencing reads in the FASTA, FASTQ or SFF formats, including Illumina, Ion Torrent and Pacific Biosciences technologies.
Proper citation: TAPyR (RRID:SCR_000588) Copy
http://mendel.stanford.edu/SidowLab/downloads/gerp/
Software that identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint. We refer to these deficits as Rejected Substitutions. Rejected substitutions are a natural measure of constraint that reflects the strength of past purifying selection on the element. GERP estimates constraint for each alignment column; elements are identified as excess aggregations of constrained columns. A false-positive rate (which is user-settable) is calculated using "shuffled" alignments in which the order of columns is randomized., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: GERP (RRID:SCR_000563) Copy
http://www.broadinstitute.org/cancer/cga/mutect
Software for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.
Proper citation: MuTect (RRID:SCR_000559) Copy
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