inst/update_notes/functionality_update.md

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

Current Functionalities v2.3.3 - 17 June 2024

1) Along with an update to the function greatAnnotate we have added the ability to run the GREAT analysis locally. 2) Updated the vis-graph3d javascript packaged used within the interactome3D. 3) Fixed a bug in interactome3D where only every 5th TF was labelled. 4) Fixed a bug where a local database request returned an empty objected. 5) Fixed a bug present when user submitted peaks where provided to intersectPeakMatrix.

Previous Version

Functionalities version 2.3.2 - 3 June 2024

1) Retired rbokeh HTML output due to the package no longer being maintain. 2) Recreated the HTML output of greatAnnotate using the three new packages: plotly, crosstalk, and DT.

Functionalities version 2.3.1 - 26 April 2024

Removed deprecated format for aes data in ggplot2.

Functionalities version 2.3.0 - 16 April 2024

bug fixed allowing for backwards compatibility with older local database versions.

Functionalities version 2.2.3 - 8 March 2024

bug fixed within .searchMotif.

Functionalities version 2.2.2 - 29 February 2024

1) Fixed export error for apiRequest. 2) Exported formMatrixFromSeq for the forkedTF R library.

Functionalities version 2.2.1 - 23 January 2024

1) Built a class to handle all server side or local calls to the Tregulome compendium. 2) Replaced all deprecated compendium calls with a class instantiation and/or method call to the new apiClass.

Functionalities version 2.2.0 - 19 December 2023

1) Overhauled the MEME and TRANSFAC functionality throughout the package. 2) Modularized intersectPeakMatrix to allow for integration within the forkedTF R library. 3) Exported previously hidden helper functions for the forkedTF R library.

Functionalities version 2.1.2 - 24 May 2023

bug fixed within intersectPeakMatrix ability to save MethMotif logos.

Functionalities version 2.1.1 - 4 May 2023

Bug fixed in local_db_path argument.

Functionalities version 2.1.0 - 24 April 2023

1) Added new feature to call a local version of the TFregulome compendium allowing for faster execution speeds. 2) Functionality rolled out as argument local_db_path to commonPeaks, dataBrowser, exclusivePeaks, genomeAnnotate, greatAnnotate, intersectPeakMatrix, loadPeaks, motifDistrib, searchMotif, and toTFBSTools. 3) The local version of TFregulome's database can be found here

Functionalities version 2.0.2 - 17 April 2022

Changed to Canada server as default (Singapore server retired)

Functionalities version 2.0.1 - 7 May 2021

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)

benoukraflab/TFregulomeR documentation built on July 8, 2024, 5:03 p.m.