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http://www.mhh.de/acghtool.html
A software tool for the normalization, visualization, breakpoint detection, and comparative analysis of array-CGH data which allows the accurate and sensitive detection of CNAs.
Proper citation: aCGHtool (RRID:SCR_010915) Copy
https://earray.chem.agilent.com/cghanalytics/index.html
A comprehensive design and analysis tool for setting up and interpreting your microarray experiments.
Proper citation: Agilent Genomic Workbench (RRID:SCR_010918) Copy
http://pages.cs.wisc.edu/~kliang/DBChIP/
Detects differential binding of transcription factors with ChIP-seq.
Proper citation: DBChIP (RRID:SCR_010872) 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://www.cs.ucf.edu/~xiaoman/ChIPModule/ChIPModule.html
A software tool for systematic discovery of transcription factors and their cofactors from ChIP-seq data.
Proper citation: ChIPModule (RRID:SCR_010877) 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
A short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads.
Proper citation: ERNE (RRID:SCR_010912) Copy
http://fureylab.web.unc.edu/software/fseq/
A software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser.
Proper citation: F-Seq (RRID:SCR_010880) Copy
Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.
Proper citation: HOMER (RRID:SCR_010881) Copy
http://www.raetschlab.org/suppl/palmapper
Computes both spliced and unspliced alignments at high accuracy while taking advantage of base quality information and splice site predictions.
Proper citation: PALMapper (RRID:SCR_011466) Copy
http://www.bioconductor.org/packages/release/bioc/html/ExiMiR.html
R functions for the normalization of Exiqon miRNA array data.
Proper citation: ExiMiR (RRID:SCR_012753) Copy
http://sourceforge.net/projects/cnv/
Software for a web-enabled platform for analyzing genome variation such as copy number variation (CNV).
Proper citation: CNV Workshop (RRID:SCR_012635) Copy
http://www.bioconductor.org/packages/release/bioc/html/motifRG.html
Software tools for discriminative motif discovery using regression methods.
Proper citation: motifRG (RRID:SCR_012602) Copy
http://www.bioconductor.org/packages/release/bioc/html/MiRaGE.html
Software package that contains functions for inference of target gene regulation by miRNA, based on only target gene expression profile.
Proper citation: MiRaGE (RRID:SCR_012738) Copy
http://bioconductor.org/packages/release/bioc/html/DEXSeq.html
Software package focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.
Proper citation: DEXSeq (RRID:SCR_012823) Copy
http://www.bioconductor.org/packages/release/bioc/html/CexoR.html
Software for strand specific peak-pair calling in ChIP-exo replicates.
Proper citation: CexoR (RRID:SCR_012769) Copy
http://bioconductor.org/packages/edgeR/
Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.
Proper citation: edgeR (RRID:SCR_012802) Copy
http://tare.medisin.ntnu.no/motiflab/
Software for a general workbench for analyzing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules.
Proper citation: MotifLab (RRID:SCR_012649) Copy
Integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies.
Proper citation: KEGG (RRID:SCR_012773) Copy
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