Package: TFARM 1.29.0

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:Liuba Nausicaa Martino, Alice Parodi, Gaia Ceddia, Piercesare Secchi, Stefano Campaner, Marco Masseroli

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# Install 'TFARM' in R:
install.packages('TFARM', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • DELTA - Contains the delta variations of support, confidence and lift.
  • IMP - Contains the mean Importance Index of each co-regulator.
  • IMP_Z - Contains the Importance Index associated with each co-regulator which is present in at least one association rule.
  • I_c_2 - Contains the mean Importance Index of pairs of transcription factors which are 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.
  • TF_Imp - Contains the candidate co-regulators and the number of rules associated with them.
  • imp_FOSL2 - Contains the set of Importance Indexes of FOSL2 in a given set of rules.
  • 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_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.
  • r_noFOSL2 - Represents an example of rulesTF0 output, where the presence of FOSL2 was replaced with its absence.

On BioConductor:TFARM-1.29.0(bioc 3.21)TFARM-1.28.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

biologicalquestioninfrastructurestatisticalmethodtranscription

4.00 score 2 scripts 202 downloads 11 exports 40 dependencies

Last updated 23 days agofrom:da642eb769. Checks:OK: 2 NOTE: 2 WARNING: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxNOTEOct 31 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winWARNINGOct 31 2024
R-4.3-macOKOct 31 2024

Exports:distribVizheatIICompIPCAitemsitemsetpresAbsrulesGenrulesTFrulesTF0search_rule

Dependencies:arulesaskpassBiocGenericsbitopscaToolsclicurldotCall64fieldsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluegplotsgtoolshttrIRangesjsonliteKernSmoothlatticelifecyclemagrittrmapsMatrixmimeopensslR6RcpprlangS4VectorsspamstringistringrsysUCSC.utilsvctrsviridisLiteXVectorzlibbioc

Transcription Factor Association Rule Miner

Rendered fromTFARM.Rnwusingknitr::knitron Oct 31 2024.

Last update: 2019-06-24
Started: 2016-11-04

Readme and manuals

Help Manual

Help pageTopics
Contains the delta variations of support, confidence and lift.DELTA
Boxplots visualization of the Importance Index distribution of a set of transcription factors.distribViz
Generates an heatmap visualization of the mean Importance Index of pairs of transcription factors.heatI
Contains the mean Importance Index of pairs of transcription factors which are present in at least one association rule.I_c_2
Computes the Importance Index of a transcription factor in a set of association rules.IComp
Contains the mean Importance Index of each co-regulator.IMP
Contains the set of Importance Indexes of FOSL2 in a given set of rules.imp_FOSL2
Contains the Importance Index associated with each co-regulator which is present in at least one association rule.IMP_Z
Principal Components Analysis for distributions of variations of support and confidence obtained removing a transcription factor from a set of rules.IPCA
Extracts items in the left-hand-side of an association rule.items
Builds the itemset in the left-hand-side of an association rule.itemset
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.MCF7_chr1
Contains co-regulators found in at least one association rule.p_TFs
Splits a set of transcription factors in 'present' or 'absent' transcription factors in a set of rules.presAbs
Represents an example of rulesTF output, i.e. the subset of rules whose left-hand-sides contain FOSL2, and the correspondent quality measures.r_FOSL2
Represents an example of rulesTF0 output, where the presence of FOSL2 was replaced with its absence.r_noFOSL2
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.r_TEAD4
Exctracts relevant association rules.rulesGen
Extracts a subset of rules that contain a certain transcription factor (or a combination of transcription factors) in their left-hand-side.rulesTF
Substitutes the presence of a transcription factor (or a combination of transcription factors) in the left-hand-side of a set of rules, with its absence.rulesTF0
Finds an association rule in a dataset.search_rule
Contains the candidate co-regulators and the number of rules associated with them.TF_Imp