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http://www.uwyo.edu/buerkle/software/bamova/

Software that implements a Bayesian Analysis of Molecular Variance and different likelihood models for three different types of molecular data (including two models for high throughput sequence data).

Proper citation: bamova (RRID:SCR_000510) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/foursig/

A suite of software programs for analyzing and visualizing 4C-seq data.

Proper citation: fourSig (RRID:SCR_000516) Copy   

•   Source: SciCrunch Registry
  

http://www.molmine.com/magma/

A collection of cook-book like manuals for various microarray designs. MAGMA is a collaboration between the Norwegian Microarray Consortium NMC and MolMine AS

Proper citation: Mini Analysis Guide for Microarrays (RRID:SCR_000596) Copy   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

http://www.tapyr.net/

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   

•   Source: SciCrunch Registry
  

http://metagenomics.atc.tcs.com/SPHINX/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Hybrid binning tool that achieves high binning efficiency by utilizing both "compositional" and "similarity" features of the query sequence during the binning process. SPHINX can analyze sequences in metagenomic data sets as rapidly as composition based approaches, but nevertheless has the accuracy and specificity of similarity based algorithms., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SPHINX (RRID:SCR_000534) Copy   

•   Source: SciCrunch Registry
  

http://open-ms.sourceforge.net/documentation/knime-integration/

A graphical user interface (GUI) for rapid composition of HPLC-MS analysis workflows. Workflow construction is reduced to drag-and-drop of analysis tools and adding connections in between.

Proper citation: TOPPAS (RRID:SCR_000533) Copy   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

http://www.ijbcb.org/ESPRITPIPE/php/onlinetool.php

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9, 2022. Software tool for estimating Species Richness Using 16S rRNA Pyrosequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ESPRIT (RRID:SCR_000552) Copy   

•   Source: SciCrunch Registry
  

http://thomsonreuters.com/metadrug/

A leading systems pharmacology solution that incorporates extensive manually curated information on biological effects of small molecule compounds. Predictive and analytical algorithms look at chemical compounds from different angles in one integrated workflow are available for: * Individual previously described compounds to look up their known information and predict currently unknown properties * Individual newly synthesized or isolated compounds to predict their properties from its structures * Compound libraries to extract known and predict new properties of individual compounds and perform their comparison and prioritization

Proper citation: MetaDrug (RRID:SCR_000461) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/reprever/?source=directory

Software that identifies (a) the insertion breakpoints where the extra duplicons inserted into the donor genome and (b) the actual sequence of the duplicon for any genomic regions that are increased in copy number.

Proper citation: Reprever (RRID:SCR_000463) Copy   

•   Source: SciCrunch Registry
  

https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/ng6/index.php/Pyrocleaner

A software module for cleaning 454 pyrosequencing reads using filters such as read duplication, length, complexity, base-pair quality and number of undetermined bases. The software also uses flowgram files of paired-end sequences to validate paired-ends files of another file.

Proper citation: Pyrocleaner (RRID:SCR_000584) Copy   

•   Source: SciCrunch Registry
  

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

An R package developed for the large-scale analysis of gene expression signatures. It gives the implementations of the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. And its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest.

Proper citation: GeneExpressionSignature (RRID:SCR_000455) Copy   

•   Source: SciCrunch Registry
  

https://github.com/PacificBiosciences/pbcore

Software Python library for reading and writing PacBio data files.

Proper citation: pbcore (RRID:SCR_000454) Copy   

•   Source: SciCrunch Registry
  

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. Software that provides quality control and quality assessment tools for flow cytometry data.

Proper citation: flowQ (RRID:SCR_000575) Copy   

•   Source: SciCrunch Registry
  

http://web.expasy.org/sulfinator/

Data analysis service that predicts tyrosine sulfation sites in protein sequences.

Proper citation: Sulfinator (RRID:SCR_000452) Copy   

•   Source: SciCrunch Registry
  

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

Algorithm for testing significance of clustering in RNA-seq data.

Proper citation: SigFuge (RRID:SCR_000444) Copy   

•   Source: SciCrunch Registry
  

http://wannovar.usc.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web interface to the ANNOVAR software, a tool to annotate functional consequences of genetic variation from high-throughput sequencing data, to help biologists without bioinformatics skills to easily submit a list of mutations (even whole-genome variants calls) to the web server, select the desired annotation categories, and receive functional annotation back by emails. Given a list of single nucleotide variants (SNVs) and insertions / deletions in VCF or ANNOVAR input format, wANNOVAR annotates their functional effects on genes (such as amino acid changes for non-synonymous SNPs), calculate their predicted functional importance scores (such as SIFT and PolyPhen scores), retrieve allele frequencies in public databases (such as the 1000 Genomes Project and NHLBI-ESP 6500 exomes), and implement a variants reduction protocol to identify a subset of potentially deleterious variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: wANNOVAR (RRID:SCR_000565) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/virema/

Software Python package for detection, alignment and reporting of recombination events in Next-Generation Sequencing data. Detects and reports recombination or fusion events in virus genomes using deep sequencing datasets.

Proper citation: ViReMa (RRID:SCR_000566) Copy   

•   Source: SciCrunch Registry