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http://www.wageningenur.nl/en/show/Pedimap.htm
A software tool for visualizing phenotypic and genotypic data for related individuals linked in pedigrees.
Proper citation: Pedimap (RRID:SCR_010796) Copy
http://www.ngsbicocca.org/html/ceqer.html
A graphical, event-driven tool for CNA/AI-coupled analysis of exome sequencing reads.
Proper citation: CEQer (RRID:SCR_010813) Copy
http://bg.upf.edu/group/projects/oncodrive-fm.php
An approach to uncover driver genes or gene modules.
Proper citation: Oncodrive-fm (RRID:SCR_010781) Copy
http://www.bcgsc.ca/platform/bioinfo/software/ssake
Software designed to help leverage the information from short sequences reads by stringently clustering them into contigs that can be used to characterize novel sequencing targets.
Proper citation: SSAKE (RRID:SCR_010753) Copy
http://www.embl.de/~korbel/CopySeq/
A computational tool that analyzes the depth-of-coverage of high-throughput DNA sequencing reads, and can integrate paired-end and breakpoint junction analysis based CNV-analysis approaches, to infer locus copy-number genotypes.
Proper citation: CopySeq (RRID:SCR_010758) Copy
https://github.com/ekg/freebayes
A Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, MNPs, and complex events smaller than the length of a short-read sequencing alignment.
Proper citation: FreeBayes (RRID:SCR_010761) Copy
http://bioinfo-out.curie.fr/projects/micsa/
A software package for the identification of transcription factor binding sites in ChIP-Seq data, developed by Computational Systems Biology of Cancer group at the Bioinformatics Laboratory of Institut Curie (Paris).
Proper citation: MICSA (RRID:SCR_010860) Copy
http://www.cs.ucr.edu/~polishka/
A command line software tool for accurate placing of the nucleosomes using a Modified Gaussian Mixture Model. It was designed to resolve overlapping nucleosomes and extract extra information (fuzziness, probability, etc.) of nucleosome placement. To achieve this goal the tool clusters the input tags according to Nucleosome Model (see the paper for detailed description) using EM learning process. The tool is written in C++. There are no special requirements except for g++ compiler and *nix environment to compile and use the tool. It was checked to compile using g++ compiler under Ubuntu 11.04 and Mac OS X 10.6
Proper citation: NOrMAL (RRID:SCR_010889) Copy
https://launchpad.net/asterias
A set of web-based applications for the analysis of genomic and proteomic data. Asterias combines Python with R and C/C++, using MPI for parallelization, and aspires to become a standard for high-performance, distributed, web-based bioinformatics and biostatistics applications.
Proper citation: Asterias (RRID:SCR_010936) Copy
A user-friendly analysis software for high-throughput data.
Proper citation: Chipster (RRID:SCR_010939) Copy
http://methmarker.mpi-inf.mpg.de/
Tool that facilitates the design and optimization of gene-specific DNA methylation assays. Beyond its use as an epigenetic primer-design tool, it provides extensive support for epigenetic biomarker optimization. Download MethMarker or start it directly from within your web browser.
Proper citation: MethMarker (RRID:SCR_010908) Copy
Anl algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments.
Proper citation: SISSRs (RRID:SCR_010866) Copy
http://code.google.com/p/zinba/
Software to identify genomic regions enriched in a variety of ChIP-seq and related next-generation sequencing experiments (DNA-seq), calling both broad and narrow modes of enrichment across a range of signal-to-noise ratios. ZINBA models and accounts for factors that co-vary with background or experimental signal, such as G/C content, and identifies enrichment in genomes with complex local copy number variations. ZINBA provides a single unified framework for analyzing DNA-seq experiments in challenging genomic contexts.
Proper citation: ZINBA (RRID:SCR_010868) Copy
An R package for analyzing large Affymetrix data sets.
Proper citation: Aroma.affymetrix (RRID:SCR_010919) Copy
http://bioinfo.au.tsinghua.edu.cn/software/NURD/
An algorithm to inference isoform expression., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: NURD (RRID:SCR_010988) Copy
https://github.com/hangyabalazs/opeth
Software tool to enable flexible online visualization of action potential alignment to external events. Performs spike detection based on raw Open Ephys data exported via ZeroMQ. Requires triggers from Open Ephys for histogram display as spikes are detected around them.
Proper citation: Online Peri-Event Time Histogram for Open Ephys (RRID:SCR_018022) Copy
https://github.com/PapenfussLab/bionix
Software tool for reproducible bioinformatics that unifies workflow engines, package managers, and containers. Implemented as lightweight library on top of Nix deployment system. Bioinformatics workflows in functional Nix language.
Proper citation: BioNix (RRID:SCR_017662) Copy
https://laniakea-elixir-it.github.io/
Software tool for automatic deployment of virtual Galaxy environments for life science. Can be deployed over common cloud architectures supported both by public and private e-infrastructures. User interacts with Laniakea based service through simple front end that allows general setup of Galaxy instance, then Laniakea takes care of automatic deployment of virtual hardware and software components. User gains access with full administrative privileges to private, production grade, fully customized, Galaxy virtual instance, and to underlying virtual machine.
Proper citation: Laniakea (RRID:SCR_018146) Copy
A C++ library for parsing and manipulating Variant Call Format (VCF) files, and many command-line utilities. The API provides a quick and extremely permissive method to read and write VCF files. Extensions and applications of the library provided in the included utilities (*.cpp) comprise the vast bulk of the library's utility for most users.
Proper citation: vcflib (RRID:SCR_001231) Copy
http://www.neuroepigenomics.org/methylomedb/
A database containing genome-wide brain DNA methylation profiles for human and mouse brains. The DNA methylation profiles were generated by Methylation Mapping Analysis by Paired-end Sequencing (Methyl-MAPS) method and analyzed by Methyl-Analyzer software package. The methylation profiles cover over 80% CpG dinucleotides in human and mouse brains in single-CpG resolution. The integrated genome browser (modified from UCSC Genome Browser allows users to browse DNA methylation profiles in specific genomic loci, to search specific methylation patterns, and to compare methylation patterns between individual samples. Two species were included in the Brain Methylome Database: human and mouse. Human postmortem brain samples were obtained from three distinct cortical regions, i.e., dorsal lateral prefrontal cortex (dlPFC), ventral prefrontal cortex (vPFC), and auditory cortex (AC). Human samples were selected from our postmortem brain collection with extensive neuropathological and psychopathological data, as well as brain toxicology reports. The Department of Psychiatry of Columbia University and the New York State Psychiatric Institute have assembled this brain collection, where a validated psychological autopsy method is used to generate Axis I and II DSM IV diagnoses and data are obtained on developmental history, history of psychiatric illness and treatment, and family history for each subject. The mouse sample (strain 129S6/SvEv) DNA was collected from the entire left cerebral hemisphere. The three human brain regions were selected because they have been implicated in the neuropathology of depression and schizophrenia. Within each cortical region, both disease and non-psychiatric samples have been profiled (matching subjects by age and sex in each group). Such careful matching of subjects allows one to perform a wide range of queries with the ability to characterize methylation features in non-psychiatric controls, as well as detect differentially methylated domains or features between disease and non-psychiatric samples. A total of 14 non-psychiatric, 9 schizophrenic, and 6 depression methylation profiles are included in the database.
Proper citation: MethylomeDB (RRID:SCR_005583) Copy
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