• 资源导航
  • ChIP-Seq
1. ERANGE
ERANGE is a Python package for doing RNA-seq and ChIP-seq.
标签：RNA-Seq Alignment, RNA-Seq Quantitation, ChIP-Seq,Allele-specific transcription
2. CHiPSeq
From Science Johnson, 2007
标签：ChIP-Seq
3. macs
Model-based Analysis of ChIP-Seq data. Model-based Analysis of ChIP-Seq (MACS): for identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and MACS improves the spatial resolution of bindi...
标签：ChIP-Seq
4. EdgeR
edgeR is an R/Bioconductor software package for statistical analysis of replicated count data. Methods are designed for assessing differential expression in comparative RNA-Seq experiments, but are generally applicable to count data from other genome-scale platforms (ChIP-Seq, MeDIP-Seq...
标签：RNA-Seq, RNA-Seq Quantitation,ChIP-Seq, Gene Expression Analysis, DNA methylation
5. DESeq
DESeq is an R package to analyse count data from high-throughput sequencing assays such as RNA-Seq and test for differential expression. The latest version is DESeq2 (released April 2013).
标签：RNA-Seq Quantitation, ChIP-Seq
6. CisGenome
An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis
标签：ChIP-Seq, ChIP-on-chip, Motif analysis, Gene annotation retrieval
7. QuEST
QuEST is a Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitations (ChIP-Seq or ChIPseq).
标签：ChIP-Seq
8. Sissrs
Produce a list of peakmaxima from aligned positions.
标签：ChIP-Seq
9. FindPeaks 3.1
Findpeaks was developed to perform analysis of ChIP-Seq experiments.
标签：ChIP-Seq
10. CLCbio Genomics Workbench
De novo and reference assembly SNP and small indel detection and annotation.
标签：Genomics, Whole Genome Resequencing, De-novo assembly, SNP discovery, InDel discovery, ChIP-Seq, RNA-Seq,MiRNA, Transcriptomics
11. SeqMan NGen
Sequence assembly software using traditional, next-gen, and third-gen techonologies. Subsequent analysis of the assembly, including SNP discovery, coverage evaluation and consensus annotation is provided through full integration with Lasergene.
标签：Genomics, De-novo assembly, De novo transcriptome assembly,Whole Genome Resequencing, SNP discovery, InDel discovery,ChIP-Seq, RNA-Seq Alignment
12. SICER
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data.
标签：ChIP-Seq, Epigenomics
13. SeqSolve
Simple analysis of Next Generation Sequencing data.
标签：RNA-Seq, ChIP-Seq,Transcriptomics, Small RNA transcriptome
14. DiffBind
Differential Binding Analysis of ChIP-Seq peak data Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.
标签：ChIP-Seq
15. USeq
Collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms. Initial emphasis: chIP-seq and RNA-Seq with FDR estimations
标签：ChIP-Seq, RNA-Seq Alignment
16. Sole-Search
Determines statistically significant peaks from ChIP experiments
标签：ChIP-Seq
17. NPS
Identify nucleosome positions given histone-modification ChIP-seq or nucleosome sequencing at the nucleosome level.
标签：Epigenomics, ChIP-Seq
18. BayesPeak
A Bayesian hidden Markov model to detect enriched locations in ChIP-seq data.
标签：ChIP-Seq
19. Novocraft
Novoalign is a program for mapping short reads from the Illumina/SOLiD sequencing platform(s) to a reference genome. Package for aligning short reads to reference genomes
标签：Genomics, Whole Genome Resequencing, RNA-Seq Alignment, ChIP-Seq, MiRNA
20. RSAT peak-motifs
A workflow combining a series of time- and memory-efficient motif analysis tools to extract motifs from full-size collections of peaks as generated by ChIP-seq, ChIP-chip or other ChIP-X technologies.
标签：ChIP-Seq, Regulatory genomics,Epigenomics
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