https://github.com/ay-lab/fithichip - Major Release - Version 11.0 (December 2022)

1. FitHiChIP now support HiChIP interactions in .hic and .cool / .mcool formats, in addition to the earlier formats.
2. Updated configuration files corresponding to these new input options.
3. Updated Docker and Singularity packages.
4. Differential HiChIP loop calling does not require ChIP-seq alignment files as a mandatory option. If users do not have any ChIP-seq alignment file, they can just proceed with the differential analysis without considering the difference in 1D.
5. FitHiChIP output loops are now converted to files compatible with WashU, UCSC and IGV epigenome browsers.

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Published by ay-lab over 3 years ago

https://github.com/ay-lab/fithichip - 10.0

Version 10.0 - April 2022

1) Minimum dependency of HiC-pro installation. 2) Updated parallel processing to make it robust across any computational cluster.

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Published by ay-lab about 4 years ago

https://github.com/ay-lab/fithichip - Major release - October 2021

This release provides lots of new functionalities, described in the README. Users are requested to use this updated version.

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Published by ay-lab almost 5 years ago

https://github.com/ay-lab/fithichip - Updated release

Release 9.0 (January 10, 2021)

1. Updated singularity, Docker installation, incorporating the latest code and dependencies.
2. Incorporated simultaneous generation of WashU browser compatible tracks for differential analysis.
3. Minor warning fix regarding 0 size of input peaks for a given chromosome.
4. Updated documentation.

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Published by ay-lab over 5 years ago

https://github.com/ay-lab/fithichip - Minor updates

Corresponds to the minor updates in the version 8.1 (May 2020)

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Published by ay-lab about 6 years ago

https://github.com/ay-lab/fithichip - Published version - Nature Communications

Release 8.0 - Encapsulates releases 7.1 and 7.0 as well

(For detailed list of changes, please see the Release Notes)

1) Updated differential analysis module, with bedgraph / bam formatted ChIP data support - much lower running time 2) Support for HiC data 3) Support for HiChIP data simulation from input ChIP and HiC data 4) Support for locus pairs with contact count as an input format

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Published by ay-lab over 6 years ago

https://github.com/ay-lab/fithichip - BiorXiv 2nd version

Support for peak header; updated spline fit plots; minor big fixes

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Published by ay-lab over 7 years ago

https://github.com/ay-lab/fithichip - Minor upgrade with summary

This release corresponds to the BiorXiv version, with the following upgrades:

1) Creation of a summary .html file in the specified output directory. This summary file lists all the important output files the user should check, including the significant interactions. It also plots distribution of interactions according to the genomic distance, FDR thresholds, etc.

2) Support for gzipped file in the validpairs input, matrix input (from HiC-pro) and also for the input peak file. It'll enable users to save storage space.

3) Minor fix in the parsing configuration file routine.

4) Minor modification in the spline and interaction plots.

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Published by ay-lab almost 8 years ago

https://github.com/ay-lab/fithichip - Release - BioRxiv version

This release contains updated FitHiChIP code with the following changes, and corresponds to the manuscript published as BioRxiv:

1) Added a new module for differential analysis of two categories of FitHiChIP loops, each with multiple replicates. 2) Included a separate script for peak calling from the HiChIP data itself, for use in the significance estimation. 3) Added various utility scripts for producing contact matrix of varying resolutions, merging ChIP-seq alignments, and generating ChIP-seq coverage of individual replicates. These files are all used for the proposed differential analysis. 4) Minor bug fix in the merging adjacent loop code. 5) Added functionality of plotting distance vs contact count for the significant loops. 6) Discarded various redundant parameters from the configuration file and the code implementation.

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Published by ay-lab almost 8 years ago

https://github.com/ay-lab/fithichip - Release - removed unnecessary dependencies

1) Reference files such as fasta sequence (corresponding to the reference genome), mappability file, restriction fragment file, are made as optional parameters. User can proceed without specifying these parameters (keeping the entries blank in the configuration file). The output interaction file is of the same format as before, except that, without any such genome specific input files, those fields have 0 values.

2) Minor fix in coverage computation (support for gzipped / plain text valid pairs file)

3) Optional plotting of mappability, GC content, and RE sites, according to the parameter specifications.

4) Updated configuration file.

5) Updated README file.

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Published by ay-lab over 8 years ago

https://github.com/ay-lab/fithichip - FitHiChIP major release

This version contains a major upgrade of both methodology and configuration parameters:

1) implements a novel bias regression technique, in addition to original distance decay modeling, to find out the statistical significant interactions. 2) Supports both coverage specific bias normalization, as well as normalization using ICE. 3) Implements a novel peak to peak background specific interaction detection, and applies it specifically for peak to all (default) interaction modeling. The proposed background modeling is found to significantly reduce the number of false positive interactions. 3) Supports overwriting existing FitHiChIP outputs (if user wants to overwrite the existing output files with a new execution)

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Published by ay-lab over 8 years ago

https://github.com/ay-lab/fithichip - FitHiChIP + HiCPro - Release 3.0

Changes done in this release:

1) Main executable is modified for more stringent checking of the input paramters, HiC-Pro installation directory. 2) Minor changes of the source code of merging nearby interactions. 3) Updating sample configuration file and sample test scripts. 4) Bedtools latest version (2.26) support and corresponding adjustment in the code

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Published by ay-lab over 8 years ago

https://github.com/ay-lab/fithichip - FitHiChIP_HiCPro - 2nd release

Updated code with the following modifications:

1) Updated bias correction routines with peak and non-peak specific bias values. 2) Added an optional routine of merging the nearby interactions. If user opts this option, interactions whose both ends are very close (within a bin) are represented as a single interaction. 3) Minor bug fix regarding the distance threshold settings.

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Published by ay-lab over 8 years ago

https://github.com/ay-lab/fithichip - FitHiChIP_HiCPro - 1st release

Software to analyze HiChIP data, by getting the statistical significant interactions using FitHiC. The input paired end reads are provided from the HiC-Pro package. The pipeline creates the interaction matrix, considers CIS interactions within a specified distance range, applies FitHIC on the raw contact count, and also generates filtered interactions using a bias correction method.

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Published by ay-lab almost 9 years ago