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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://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
  

https://www.openmicroscopy.org/site/products/bio-formats

Standalone software Java library for reading microscopy image data files in any format and writing image data using standardized, open formats. It currently reads and converts more than 120 file formats to the OME-TIFF data standard.

Proper citation: Bio-Formats (RRID:SCR_000450) 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://sourceforge.net/projects/srma/

A post-alignment micro re-aligner for next-generation high throughput sequencing data.

Proper citation: SRMA (RRID:SCR_000669) Copy   

•   Source: SciCrunch Registry
  

http://neuralensemble.org/trac/OpenElectrophy

Software Python module for electrophysiology data analysis.

Proper citation: OpenElectrophy (RRID:SCR_000819) Copy   

•   Source: SciCrunch Registry
  

https://bitbucket.org/mckinsel/shortfuse

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A software package with tools for identifying fusion transcripts from RNA-Seq data. It is written in C++, and has dependencies on packages from Python 2.

Proper citation: ShortFuse (RRID:SCR_001107) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/cuda-ec/

A fast parallel error correction tool for short reads.

Proper citation: CUDA-EC (RRID:SCR_001090) Copy   

•   Source: SciCrunch Registry
  

http://sun.aei.polsl.pl/dsrc/

An application designed for compression of data files containing reads from DNA sequencing in FASTQ format. Its main features include multithreaded compression of FASTQ output, python and C++ libraries, and support for lossy IDs compression.

Proper citation: DSRC (RRID:SCR_001005) Copy   

•   Source: SciCrunch Registry
  

http://jbrowse.org/

A high-performance visualization tool for interactive exploration of large, integrated genomic datasets written primarily in JavaScript. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

Proper citation: JBrowse (RRID:SCR_001004) Copy   

•   Source: SciCrunch Registry
  

http://131.174.198.125/bioinfo/gimmemotifs/

Software that provides a de novo motif prediction pipeline, especially suited for ChIP-seq datasets. It incorporates several existing motif prediction algorithms in an ensemble method to predict motifs and clusters these motifs using the WIC similarity scoring metric., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GimmeMotifs (RRID:SCR_001146) Copy   

•   Source: SciCrunch Registry
  

http://dna.leeds.ac.uk/illuminator/

A sequence alignment program for the output from Illumina GA-II clonal sequencers. It uses an algorithm that indexes the reference sequence as a series of 8-mers and then matches the genomic reads to the 8-mer index, in a mutation-tolerant way permitting identification of single-nucleotide substitutions and indels.

Proper citation: Illuminator (RRID:SCR_001019) Copy   

•   Source: SciCrunch Registry
  

https://immersive-analytics.infotech.monash.edu/vanted/

Software tool for extendable network visualization and analysis for the life sciences. It is Java-based and allows users to create, edit and map data onto existing or new networks. Experimental datasets can be visualized on network elements as graphical charts to show time series data or data of different treatments, as well as environmental conditions in the context of the underlying biological processes. Users can utilize built-in statistical algorithms to evaluate mapped data.

Proper citation: Visualization and Analysis of Networks containing Experimental Data (VANTED) (RRID:SCR_001138) 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://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
  

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://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