Software

• GFold
  Generalized fold change for ranking differentially expressed genes from RNA-seq data.
• BINOCh
  Binding Inference from Nucleosome Occupancy Changes
• Cistrome
  A web-based integrative platform for transcriptional regulation studies, from peak calling, correlation and association studies, expression analyses, to motif discovery.
• Model-based Analysis of ChIP-Seq (MACS)
  A model-based algorithm for finding enriched regions in ChIP-Seq experiments
• Nucleosome Positioning from Sequencing (NPS)
  A signal processing-based algorithm for identifying positioned nucleosomes fromsequencing experiments at the nucleosome level
• Cis-regulatory Element Annotation System(CEAS) - Standalone version
  A standalone Python package for analyzing ChIP-chip/seq data
• SAGE-seq gene EXPRESSion analysis pipelines (sageExpress)
  Gene expression analysis pipelines for SAGE-Seq including tag mapping, novel normalization method using empirical Bayes and differential gene analysis
• Cis-regulatory Element Annotation System(CEAS)
  An integrated webserver for analyzing ChIP-chip data
• Model-based Analysis of 2-Color Arrays (MA2C)
  A model-based algorithm for analyzing 2-color microarrays.
• Model-based Analysis of Tiling-array (MAT)
  A model-based algorithm for finding enriched regions in ChIP-Chip experiments
• extreme MApping of OligoNucleotides (xMAN)
  A simple and efficient method for the mapping of millions of queryoligonucleotide fragments to the subject genome of any given length, at leastan order of magnitude faster than other popular existing tools
• Hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays (HMMTiling)
  HMMTiling is a comprehensive software package for tiling array data analysis. It includes command line python applications for filtering, mapping, quantile-normalizing and enriched-region identification from ChIP-chip experiments on tiling arrays. (Download)
• Microarray Blob Remover (MBR)
  A microarray JAVA tool which allows rapid visualization, detection, and removalof blob-like defects as an initial quality control step
• CompareProspector
  A sequence motif-finding algorithm
• Motif Regressor
  A program for finding DNA sequence motifs
• MDscan
  A Fast and Accurate Motif Finding Algorithm With Applications To Chromatin Immunoprecipitation Microarray Experiments
• BioProspector
  Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-ExpressedGenes

Resource

• CistromeMap
  A knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human.




Last modified by JR May 1, 2012