:: DESCRIPTION
SraTailor is a simple GUI software for visualizing published ChIP-seq raw data
::DEVELOPER
Department of Developmental Biology, Kyushu University
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genes Cells. 2014 Dec;19(12):919-26. doi: 10.1111/gtc.12190. Epub 2014 Oct 17.
SraTailor: graphical user interface software for processing and visualizing ChIP-seq data.
Oki S1, Maehara K, Ohkawa Y, Meno C.
:: DESCRIPTION
ABC is a computational tool that identifies allele specific binding of transcription factors from aligned ChIP-Seq reads at heterozygous SNVs.
::DEVELOPER
The Computational Biology and Medicine Program (CBMP)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
ABC: A tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments.
Bailey SD, Virtanen C, Haibe-Kains B, Lupien M.
Bioinformatics. 2015 May 20. pii: btv321.
:: DESCRIPTION
PeakRanger detects enriched regions from ChIP-Seq experiments and also detect summits within these regions. The software is faster than most existing peak callers while consuming less memories.
::DEVELOPER
developed in Dr.Lincoln Stein’s lab at OICR and is now in continual development at Dr.Helen Hobbs’s lab of the McDermott Center of UT Southwestern.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2011 May 9;12:139. doi: 10.1186/1471-2105-12-139.
PeakRanger: a cloud-enabled peak caller for ChIP-seq data.
Feng X, Grossman R, Stein L.
:: DESCRIPTION
SSP (Strand-shift Profile) is a tool for quality assessment of ChIP-seq data without peak calling.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Nakato R, Shirahige K.
Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile.
Bioinformatics. 2018 Jul 15;34(14):2356-2363. doi: 10.1093/bioinformatics/bty137. PMID: 29528371.
:: DESCRIPTION
DROMPA (DRaw and Observe Multiple enrichment Profiles and Annotation) is cost-effient program for peak-calling and visualization for ChIP-seq analysis. DROMPA outputs the protein binding profile map (ChIP-reads distribution and ChIP/control enrichment profile) with genomic annotation specified in pdf or png format, which can be easily handled and processed by users with little bioinformatics background. DROMPA has an associated program named parse2wig, which preprocesses the map file into wig files. This two-step procedure can drastically reduce the computational memory and time required, which makes enable to analyze large-scale ChIP-seq data (e.g., more than 10 human samples and/or multiple executions for each sample with trial-and-error) on a conventional desktop computer.
DROMPAplus is an update of DROMPA3. It is written in C++ and runs from a single launch command on conventional Linux systems.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Nakato R, Sakata T.
Methods for ChIP-seq analysis: A practical workflow and advanced applications.
Methods. 2021 Mar;187:44-53. doi: 10.1016/j.ymeth.2020.03.005. Epub 2020 Mar 30. PMID: 32240773.
Genes Cells. 2013 Jul;18(7):589-601. doi: 10.1111/gtc.12058.
DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data.
Nakato R, Itoh T, Shirahige K.
:: DESCRIPTION
BIDCHIPS is a software for quantifying and Removing Biases in ChIP-Seq Signals
::DEVELOPER
Perkins Lab at the OHRI
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BIDCHIPS: bias decomposition and removal from ChIP-seq data clarifies true binding signal and its functional correlates.
Ramachandran P, Palidwor GA, Perkins TJ.
Epigenetics Chromatin. 2015 Sep 17;8:33. doi: 10.1186/s13072-015-0028-2.
:: DESCRIPTION
Q is a fast saturation-based ChIP-seq peak caller. Q works well in conjunction with the irreproducible discovery rate (IDR) procedure.
::DEVELOPER
The Computational Biology @ Charité Berlin
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Res. 2015 Sep;25(9):1391-400. doi: 10.1101/gr.189894.115.
Saturation analysis of ChIP-seq data for reproducible identification of binding peaks.
Hansen P, Hecht J, Ibrahim DM, Krannich A, Truss M, Robinson PN.
:: DESCRIPTION
GEM (Genome wide Event finding and Motif discovery) is a software tool to study protein-DNA interaction using ChIP-Seq/ChIP-exo data. GEM resolves ChIP data into explanatory motifs and binding events at unsurpassed spatial resolution by linking binding event discovery and motif discovery with positional priors in the context of a generative model of ChIP data and genome sequence.
:: DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Yuchun Guo, Georgios Papachristoudis, Robert C Altshuler, Georg K Gerber, Tommi S Jaakkola, David K Gifford & Shaun Mahony,
Discovering homotypic binding events at high spatial resolution.
Bioinformatics. 2010 Dec 15;26(24):3028-34. Epub 2010 Oct 21. PMID: 20966006.
:: DESCRIPTION
W-ChIPeaks employs a probe-based or bin-based enrichment threshold to define peaks and applies statistical methods to control the false discovery rate for identified peaks.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Feb 1;27(3):428-30. doi: 10.1093/bioinformatics/btq669. Epub 2010 Dec 7.
W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data.
Lan X, Bonneville R, Apostolos J, Wu W, Jin VX.
:: DESCRIPTION
LONUT (LOcating Non-Unique matched Tags)is a computational tool to improve the detection of enriched regions from ChIP-seq data.
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2013 Jun 25;8(6):e67788. doi: 10.1371/journal.pone.0067788. Print 2013.
LOcating non-unique matched tags (LONUT) to improve the detection of the enriched regions for ChIP-seq data.
Wang R1, Hsu HK, Blattler A, Wang Y, Lan X, Wang Y, Hsu PY, Leu YW, Huang TH, Farnham PJ, Jin VX.