Changed to Canada server as default (Singapore server retired)
bug fixed regarding http failure
- Added new TFregulomeR compendium server in Canada. Users now can choose servers between Singapore and Canada.
- linked to mouse TFregulomeR compendium in Canada server, coming soon in Singapore server.
- Modified the functions intersectPeakMatrix and intersectPeakMatrixResult to allow profiling of users' input external signals during pair-wise comparison analysis.
- 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.
- Improved the function greatAnnotate, which now allows to use peak regions in hg38 directly with rGREAT >= 1.16.1 (no need liftover package).
- Changed the function name TFBSBrowser to dataBrowser.
- More detailed information about motifs, such as consistency with exisiting database and correlation between different motif callers, added in the output of dataBrowser.
- Fixed some bugs in function cofactorReport.
- Added y axis and number of peaks with motif in the output of plotLogo.
- Browse the TFregulomeR data warehouse (TFBSBrowser)
- Load TF peaks (loadPeaks)
- Search motif matrix and DNA methylation score matrix (searchMotif)
- Plot motif or MethMotif logo (plotLogo)
- Export motif matrix and DNA methylation score matrix (exportMMPFM)
- Get context-independent peaks along with DNA methylation profiles (commonPeaks & commonPeakResult)
- Get context-dependent peaks along with DNA methylation profiles (exclusivePeaks & exclusivePeakResult)
- 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)
- 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).
- Plot the TFBS distribution in a given list of peak sets (motifDistrib & plotDistrib)
- Annotate peak genomic locations (genomeAnnotate)
- Annotate ontologies of target genes by a peak set (greatAnnotate)
- Convert a motif matrix to a PFMatrix calss object for TFBSTools package (toTFBSTools)
- Browse the TFregulomeR data warehouse (TFBSBrowser)
- Load TF peaks (loadPeaks)
- Search motif matrix and DNA methylation score matrix (searchMotif)
- Plot motif or MethMotif logo (plotLogo)
- Export motif matrix and DNA methylation score matrix (exportMMPFM)
- Get context-independent peaks along with DNA methylation profiles (commonPeaks & commonPeakResult)
- Get context-dependent peaks along with DNA methylation profiles (exclusivePeaks & exclusivePeakResult)
- Form a intersected matrix between two lists of peak sets along with DNA methylation profiles, for interactome and co-binding partner studies (intersectPeakMatrix & intersectPeakMatrixResult)
- Plot the TFBS distribution in a given list of peak sets (motifDistrib & plotDistrib)
- Annotate peak genomic locations (genomeAnnotate)
- Annotate ontologies of target genes by a peak set (greatAnnotate)
- Convert a motif matrix to a PFMatrix calss object for TFBSTools package (toTFBSTools)