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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
American multinational technology company that specializes in internet related services and products, which include online advertising technologies, search engine, cloud computing, software, and hardware. Considered one of Big Four technology companies, alongside Amazon, Apple and Facebook.
Proper citation: Google (RRID:SCR_017097) Copy
http://mrsfast.sourceforge.net/
A cache-oblivious algorithm designed to map short reads to reference genome assemblies in a fast and memory-efficient manner. It optimizes cache usage to get higher performance. Currently Supported Features: * Mistmatches, No indels * Paired-end Mapping Mode * Discordant Paired-end Mapping Mode (to be used in conjuction with Variation Hunter)
Proper citation: mrsFAST (RRID:SCR_003128) Copy
http://acgt.cs.tau.ac.il/hyden/
Software program for designing pairs of degenerate primers for a given set of DNA sequences. It works well for large input sets of genomic sequences (e.g., hundreds of sequences of length 1Kbp). It is a batch (i.e., command-line, as opposed to graphical interface) program, available for Windows XP (downloadable version) and Linux (upon request).
Proper citation: HYDEN (RRID:SCR_003126) Copy
http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html
Software package for quantitative DNA sequencing for chromosomal aberrations providing a robust, cost-effective WGS method for DNA copy number analysis. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.
Proper citation: QDNAseq (RRID:SCR_003174) Copy
https://github.com/hangelwen/miR-PREFeR
An accurate, fast, and easy-to-use plant miRNA prediction software tool using small RNA-Seq data. It utilizes expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species.
Proper citation: miR-PREFeR (RRID:SCR_003353) Copy
An algorithm for the identification of microRNA targets. Details are provided (3' UTR alignments with predicted sites, links to various public databases etc) regarding: # microRNA target predictions in vertebrates (Krek et al, Nature Genetics 37:495-500 (2005)) # microRNA target predictions in seven Drosophila species (Grn et al, PLoS Comp. Biol. 1:e13 (2005)) # microRNA targets in three nematode species (Lall et al, Current Biology 16, 1-12 (2006)) # human microRNA targets that are not conserved but co-expressed (i.e. the microRNA and mRNA are expressed in the same tissue) (Chen and Rajewsky, Nat Genet 38, 1452-1456 (2006)) co-expressed targets
Proper citation: PicTar (RRID:SCR_003343) Copy
https://github.com/mozack/abra
Software that is a realigner for next generation sequencing data. It uses localized assembly and global realignment to align reads more accurately, thus improving downstream analysis (detection of indels and complex variants in particular).
Proper citation: Assembly Based ReAligner (RRID:SCR_003277) Copy
http://www.bioconductor.org/packages/release/bioc/html/NormqPCR.html
Software package providing functions for the selection of optimal reference genes and the normalization of real-time quantitative PCR data.
Proper citation: NormqPCR (RRID:SCR_003388) Copy
http://code.google.com/p/popoolation/
A collection of tools to facilitate population genetic studies of next generation sequencing data from pooled individuals. It builds upon open source tools (bwa, samtools) and uses standard file formats (gtf, sam, pileup) to ensure a wide compatibility. PoPoolation allows to calculate Tajima's Pi, Watterson's Theta and Tajima's D for reference sequences using a sliding window approach. Alternatively these population genetic estimators may be calculated for a set of genes (provided as gtf). One of the main challenges in population genomics is to identify regions of intererest on a genome wide scale. PoPoolation will greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools.
Proper citation: PoPoolation (RRID:SCR_003495) Copy
A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context.
Proper citation: GEPAT (RRID:SCR_003597) Copy
http://jexpress.bioinfo.no/site/
Gene expression analysis software using Java.
Proper citation: J-Express (RRID:SCR_003609) Copy
Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS.
Proper citation: R Project for Statistical Computing (RRID:SCR_001905) Copy
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