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http://rubioseq.sourceforge.net/
Stand-alone and multiplatform application for the integrated analysis of NGS data. It implements pipelines for the analysis of single nucleotide and copy-number variation and bisulfite-seq and ChIP-seq experiments.
Proper citation: RUbioSeq (RRID:SCR_002508) Copy
Web based integrative platform for transcriptional regulation studies.
Proper citation: Cistrome (RRID:SCR_000242) Copy
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
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
Software Python package for analyzing diffusion data. Software library for analysis of diffusion MRI data.
Proper citation: Dipy (RRID:SCR_000029) 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
http://www.ngsbicocca.org/html/fusion_analyser.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2023. Software used to detect gene fusions from paired-end RNA-Seq data.
Proper citation: Fusion Analyser (RRID:SCR_000059) Copy
http://bioconductor.org/packages/release/bioc/html/CorMut.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software package for computing correlated mutations based on selection pressure. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network.
Proper citation: CorMut (RRID:SCR_000053) Copy
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
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
https://github.com/PacificBiosciences/pbcore
Software Python library for reading and writing PacBio data files.
Proper citation: pbcore (RRID:SCR_000454) Copy
An open mark-up language for NMR data.
Proper citation: nmrML (RRID:SCR_000467) Copy
http://neuralensemble.org/trac/OpenElectrophy
Software Python module for electrophysiology data analysis.
Proper citation: OpenElectrophy (RRID:SCR_000819) Copy
http://www.bioconductor.org/packages/release/bioc/html/pickgene.html
Software for adaptive Gene Picking for Microarray Expression Data Analysis.
Proper citation: pickgene (RRID:SCR_001331) Copy
https://vcftools.github.io/index.html
Software package for working with VCF files. Used to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.Implements various utilities for processing Variant Call Format files, including validation, merging, comparing. Provides general Perl API.
Proper citation: VCFtools (RRID:SCR_001235) Copy
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
http://www.bioconductor.org/packages/release/bioc/html/metahdep.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies.
Proper citation: metahdep (RRID:SCR_001225) Copy
http://www.bioconductor.org/packages/release/bioc/html/globaltest.html
A software package that tests groups of covariates (or features) for association with a response variable. The package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms.
Proper citation: globaltest (RRID:SCR_001256) Copy
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
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
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