1 Introduction | 2 Dataset | 3 Extraction of the most relevant associations | 4 Importance Index of a transcription factor | 5 Visualization tools
Package: TFARM 1.35.0
Liuba Nausicaa Martino
TFARM: Transcription Factors Association Rules Miner
It searches for relevant associations of transcription factors with a transcription factor target, in specific genomic regions. It also allows to evaluate the Importance Index distribution of transcription factors (and combinations of transcription factors) in association rules.
Authors:
TFARM_1.35.0.tar.gz
TFARM_1.35.0.zip(r-4.7)TFARM_1.35.0.zip(r-4.6)TFARM_1.35.0.zip(r-4.5)
TFARM_1.35.0.tgz(r-4.6-any)TFARM_1.35.0.tgz(r-4.5-any)
TFARM_1.35.0.tar.gz(r-4.7-any)TFARM_1.35.0.tar.gz(r-4.6-any)
TFARM_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
TFARM/json (API)
| # Install 'TFARM' in R: |
| install.packages('TFARM', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- DELTA - Contains the delta variations of support, confidence and lift.
- I_c_2 - Contains the mean Importance Index of pairs of transcription factors which are present in at least one association rule.
- IMP - Contains the mean Importance Index of each co-regulator.
- imp_FOSL2 - Contains the set of Importance Indexes of FOSL2 in a given set of rules.
- IMP_Z - Contains the Importance Index associated with each co-regulator which is present in at least one association rule.
- MCF7_chr1 - Contains genomic regions in the first chromosome of the MCF-7 human breast adenocarcinoma cell line at the ranges side, and the presence indexes of transcription factors in such regions at the metadata side.
- p_TFs - Contains co-regulators found in at least one association rule.
- r_FOSL2 - Represents an example of rulesTF output, i.e. the subset of rules whose left-hand-sides contain FOSL2, and the correspondent quality measures.
- r_noFOSL2 - Represents an example of rulesTF0 output, where the presence of FOSL2 was replaced with its absence.
- r_TEAD4 - Contains the association rules for the prediction of the presence of the transcription factor TEAD4 in the considered genomic regions, i.e., with TEAD4 in the right-hand-side of the association rules.
- TF_Imp - Contains the candidate co-regulators and the number of rules associated with them.
On BioConductor:TFARM-1.35.0(bioc 3.24)TFARM-1.34.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
biologicalquestioninfrastructurestatisticalmethodtranscription
Last updated from:e3d3fa6e9c. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 169 | ||
| linux-devel-x86_64 | NOTE | 248 | ||
| source / vignettes | OK | 302 | ||
| linux-release-x86_64 | NOTE | 295 | ||
| macos-release-arm64 | NOTE | 118 | ||
| macos-oldrel-arm64 | NOTE | 106 | ||
| windows-devel | NOTE | 128 | ||
| windows-release | NOTE | 147 | ||
| windows-oldrel | NOTE | 127 | ||
| wasm-release | OK | 150 |
Exports:distribVizheatIICompIPCAitemsitemsetpresAbsrulesGenrulesTFrulesTF0search_rule
Dependencies:arulesBiocGenericsbitopscaToolsclidotCall64fieldsgenericsGenomicRangesgluegplotsgtoolsIRangesKernSmoothlatticelifecyclemagrittrmapsMatrixRColorBrewerRcpprlangS4VectorsSeqinfospamstringistringrvctrsviridisLite
