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http://liulab.dfci.harvard.edu/NPS/
A python software package that can identify nucleosome positions given histone-modification ChIP-seq or nucleosome sequencing at the nucleosome level.
Proper citation: NPS (RRID:SCR_010890) Copy
http://linus.nci.nih.gov/BRB-ArrayTools.html
An integrated software package for the visualization and statistical analysis of DNA microarray gene expression data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: BRB-ArrayTools (RRID:SCR_010938) Copy
A R/Bioconductor package for a flexible and fast recognition of nucleosome positioning from next generation sequencing and tiling arrays experiments. The software is integrated with standard high-throughput genomics R packages and allows for in situ visualization as well as to export results to common genome browser formats.
Proper citation: nucleR (RRID:SCR_010895) Copy
http://genovar.sourceforge.net/
A Detection and Visualization software tool for Genomic Variants.
Proper citation: Genovar (RRID:SCR_010930) Copy
Tools for microarray quality control and pre-processing.
Proper citation: ArrayAnalysis.org (RRID:SCR_010932) Copy
http://bcb.dfci.harvard.edu/~gcyuan/MAnorm/MAnorm.htm
A robust software package for quantitative comparison of ChIP-Seq data sets.
Proper citation: MAnorm (RRID:SCR_010869) Copy
http://software.big.ac.cn/MeRIP-PF.html
A high-efficiency and easy-to-use analysis pipeline for MeRIP-Seq peak-finding at high resolution, which compares distributions of reads between immunoprecipitation sample and control sample.
Proper citation: MeRIP-PF (RRID:SCR_010904) Copy
https://code.google.com/p/batmeth/
Improved mapper for bisulfite sequencing reads on DNA methylation.
Proper citation: BatMeth (RRID:SCR_010906) Copy
You can easily align, visualize and quantify bisulfite sequence data for CpG methylation analysis.
Proper citation: QUMA (RRID:SCR_010907) Copy
http://ranger.sourceforge.net/
Software for a multi-purpose ChIP Seq peak caller.
Proper citation: PeakRanger (RRID:SCR_010863) Copy
http://biodoop-seal.sourceforge.net/
A suite of distributed software applications for aligning short DNA reads, and manipulating and analyzing short read alignments.
Proper citation: SEAL (RRID:SCR_010914) Copy
http://cran.r-project.org/web/packages/DIME/index.html
R-package for identifying differential ChIP-seq based on an ensemble of mixture models.
Proper citation: DIME (RRID:SCR_010874) Copy
http://bio-bwa.sourceforge.net/
Software for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp.
Proper citation: BWA (RRID:SCR_010910) Copy
http://sourceforge.net/apps/mediawiki/cloudburst-bio/index.php?title=CloudBurst
A new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.
Proper citation: CloudBurst (RRID:SCR_010911) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 26,2019. In October 2016, T1DBase has merged with its sister site ImmunoBase (https://immunobase.org). Documented on March 2020, ImmunoBase ownership has been transferred to Open Targets (https://www.opentargets.org). Results for all studies can be explored using Open Targets Genetics (https://genetics.opentargets.org). Database focused on genetics and genomics of type 1 diabetes susceptibility providing a curated and integrated set of datasets and tools, across multiple species, to support and promote research in this area. The current data scope includes annotated genomic sequences for suspected T1D susceptibility regions; genetic data; microarray data; and global datasets, generally from the literature, that are useful for genetics and systems biology studies. The site also includes software tools for analyzing the data.
Proper citation: T1DBase (RRID:SCR_007959) Copy
http://www.ebi.ac.uk/huber-srv/hilbert/
Software tool that allows to display very long data vectors in a space-efficient manner, allowing the user to visually judge the large scale structure and distribution of features simultaneously with the rough shape and intensity of individual features.
Proper citation: HilbertVis (RRID:SCR_007862) Copy
A cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.
Proper citation: BRIG (RRID:SCR_007802) Copy
https://www.ncbi.nlm.nih.gov/genbank/dbest/
Database as a division of GenBank that contains sequence data and other information on single-pass cDNA sequences, or Expressed Sequence Tags, from a number of organisms.
Proper citation: dbEST (RRID:SCR_008132) Copy
http://erlichlab.wi.mit.edu/lobSTR/
A software tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: lobSTR (RRID:SCR_008030) Copy
http://www.baderlab.org/Software/ActiveDriver
A statistical method for interpreting variations in protein sequence (e.g. coding SNPs in the population, SNVs in cancer genomes) in the context of protein post-translational signaling modifications.
Proper citation: ActiveDriver (RRID:SCR_008104) Copy
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