inst/update_notes/functionality_update.md

In linquynus/TFregulomeR-dev: TFregulomeR reveals transcription factors’ context-specific features and functions

Current Functionalities v2.0.2 - 17 April 2022

Changed to Canada server as default (Singapore server retired)

Previous Version

Functionalities version 2.0.1 - 7 May 2021

1) Fixed warnings in plotLogo function in accordance with new ggplot2 package. 2) bug fixed regarding http failure.

Functionalities version 2.0.0 - 5 March 2020

1) Added new TFregulomeR compendium server in Canada. Users now can choose servers between Singapore and Canada. 2) linked to mouse TFregulomeR compendium in Canada server, coming soon in Singapore server.

Functionalities version 1.2.2 - 10 January 2020

1) Modified the functions intersectPeakMatrix and intersectPeakMatrixResult to allow profiling of users' input external signals during pair-wise comparison analysis. 2) Added a new function interactome3D which could directly generate a dynamic 3D interface report showing TF interactome coupled with CpG methylation and users' input external signal values.

Functionalities version 1.2.1 - 25 October 2019

1) Improved the function greatAnnotate, which now allows to use peak regions in hg38 directly with rGREAT >= 1.16.1 (no need liftover package).

Functionalities version 1.2.0 - 6 September 2019

1) Changed the function name TFBSBrowser to dataBrowser. 2) More detailed information about motifs, such as consistency with exisiting database and correlation between different motif callers, added in the output of dataBrowser. 3) Fixed some bugs in function cofactorReport. 4) Added y axis and number of peaks with motif in the output of plotLogo.

Functionalities version 1.1.0 - 31 July 2019

1) Browse the TFregulomeR data warehouse (TFBSBrowser) 2) Load TF peaks (loadPeaks) 3) Search motif matrix and DNA methylation score matrix (searchMotif) 4) Plot motif or MethMotif logo (plotLogo) 5) Export motif matrix and DNA methylation score matrix (exportMMPFM) 6) Get context-independent peaks along with DNA methylation profiles (commonPeaks & commonPeakResult) 7) Get context-dependent peaks along with DNA methylation profiles (exclusivePeaks & exclusivePeakResult) 8) Form a intersected matrix between two lists of peak sets along with DNA methylation profiles and read enrichments, for interactome and co-binding partner studies (intersectPeakMatrix & intersectPeakMatrixResult) 9) Automatically generate a PDF report for TF co-factors along with motif sequences, DNA methylation (within motif and in 200bp regions) and read enrichments (cofactorReport). 10) Plot the TFBS distribution in a given list of peak sets (motifDistrib & plotDistrib) 11) Annotate peak genomic locations (genomeAnnotate) 12) Annotate ontologies of target genes by a peak set (greatAnnotate) 13) Convert a motif matrix to a PFMatrix calss object for TFBSTools package (toTFBSTools)

Functionalities version 1.0.0 - 7 May 2019

1) Browse the TFregulomeR data warehouse (TFBSBrowser) 2) Load TF peaks (loadPeaks) 3) Search motif matrix and DNA methylation score matrix (searchMotif) 4) Plot motif or MethMotif logo (plotLogo) 5) Export motif matrix and DNA methylation score matrix (exportMMPFM) 6) Get context-independent peaks along with DNA methylation profiles (commonPeaks & commonPeakResult) 7) Get context-dependent peaks along with DNA methylation profiles (exclusivePeaks & exclusivePeakResult) 8) Form a intersected matrix between two lists of peak sets along with DNA methylation profiles, for interactome and co-binding partner studies (intersectPeakMatrix & intersectPeakMatrixResult) 9) Plot the TFBS distribution in a given list of peak sets (motifDistrib & plotDistrib) 10) Annotate peak genomic locations (genomeAnnotate) 11) Annotate ontologies of target genes by a peak set (greatAnnotate) 12) Convert a motif matrix to a PFMatrix calss object for TFBSTools package (toTFBSTools)

linquynus/TFregulomeR-dev documentation built on April 23, 2022, 11:11 a.m.