资源导航

21. Cistrome: Galaxy-based web service for analysis of ChIP data; 标签：ChIP-on-chip, ChIP-Seq
22. SeqMINER: seqMINER is an integrated portable ChIP-seq data interpretation platform with optimized performances for efficient handling of multiple genomewide datasets. seqMINER allows comparison and integration of multiple ChIP-seq datasets and extraction of qualitative as well as quantitative inf...; 标签：ChIP-Seq
23. MICSA: Combines positional information with information on motif occurrences to better predict binding sites of transcription factors (TFs); 标签：ChIP-Seq
24. HPeak: Hidden Markov model (HMM)-based Peak-finding algorithm for analyzing ChIP-Seq data to identify protein-interacting genomic regions.; 标签：ChIP-Seq
25. ChIPMunk: ChIPMunk is a fast heuristic DNA motif digger based a on greedy approach accompanied by bootstrapping. ChIPMunk identifies the strong motif with the maximum Kullback Discrete Information Content in a given set of DNA sequences. *NEW URL* http://autosome.ru/ChIPMunk; 标签：ChIP-Seq, Motif analysis,Motif discovery
26. ZINBA: Identifies genomic regions enriched in a variety of ChIP-seq and related next-generation sequencing experiments; 标签：ChIP-Seq, DNA-Seq
27. BEADS: ChIP-Seq data normalization for Illumina; 标签：ChIP-Seq
28. Repitools: Toolbox of procedures to interrogate and visualize epigenomic data. Part of BioConductor; 标签：ChIP-Seq, ChIP-on-chip
29. GimmeMotifs: GimmeMotifs is a de novo motif prediction pipeline, especially suited for ChIP-seq datasets. It incorporates several existing motif prediction algorithms in an ensemble method to predict motifs and clusters these motifs using the WIC similarity scoring metric.; 标签：Transcription regulation,ChIP-Seq, Epigenomics
30. PeakRanger: A multi-purpose, ultrafast ChIP Seq peak caller; 标签：ChIP-Seq
31. MuMRescueLite: Probabilistically reincorporates multi-mapping tags into mapped short read data.; 标签：Genomics, ChIP-Seq
32. GPS: GPS is a high spatial resolution peak detection algorithm for ChIP-Seq data.; 标签：Genomics, ChIP-Seq,Transcription Factor Binding Site identification,Regulatory genomics epigenomics
33. PICS: PICS identifies binding event locations by modeling local concentrations of directional reads, and uses DNA fragment length prior information to discriminate closely adjacent binding events via a Bayesian hierarchical t-mixture model.; 标签：ChIP-Seq
34. NucleR: nucleR is a R/Bioconductor package for working with tiling arrays and next generation sequencing. It uses a novel aproach in this field which comprises a deep profile cleaning using Fourier Transform and peak scoring for a quick and flexible nucleosome calling; 标签：ChIP-on-chip, ChIP-Seq,Nucleosome Positioning,Epigenomics
35. S-MART: S-MART manages your RNA-Seq and ChIP-Seq data.; 标签：RNA-Seq, ChIP-Seq
36. Chipster: User-friendly NGS data analysis software with built-in genome browser and workflow functionality. Chipster includes tools for ChIP-seq, RNA-seq, miRNA-seq and MeDIP-seq analysis, and functionality for exome-seq and CGH-seq will soon be added.; 标签：ChIP-Seq, RNA-Seq, MiRNA-Seq,MeDIP-Seq
37. GeneProf: GeneProf is a web-based, graphical software suite and database resource for high-throughput-sequencing experiments (RNA-seq and ChIP-seq).; 标签：RNA-Seq, ChIP-Seq
38. GenomicTools: GenomicTools is a flexible computational platform for the analysis and manipulation of high-throughput sequencing data such as RNA-seq and ChIP-seq. A variety of mathematical operations between sets of genomic regions is implemented thereby enabling the prototyping of computational pipe...; 标签：Genomics, ChIP-Seq, RNA-Seq
39. AREM: AREM: Aligning Short Reads from ChIP-Sequencing by Expectation Maximization; 标签：ChIP-Seq
40. GEM: GEM is a java software tool to analyze transcription factor binding ChIP-Seq/ChIP-exo data. It predicts binding events, performs de novo motif discovery and use the motif to improve the binding event calling. It calls binding events right at (or very close to ) the motif positions, deco...; 标签：ChIP-Seq

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