CONDOP: Condition-Dependent Operon Predictions

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An implementation of the computational strategy for the comprehensive analysis of condition-dependent operon maps in prokaryotes proposed by Fortino et al. (2014) <DOI:10.1186/1471-2105-15-145>. It uses RNA-seq transcriptome profiles to improve prokaryotic operon map inference.

Author
Vittorio Fortino <vittorio.fortino@ttl.fi>
Date of publication
2016-02-24 15:47:51
Maintainer
Vittorio Fortino <vittorio.fortino@ttl.fi>
License
GPL-3
Version
1.0

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Man pages

comp.gene.transc.levels
Compile the transcription levels for the coding regions.
comp.igr.transc.levels
Compile the transcription levels for the intergenic regions.
compile.confirmed.operons
Compile a set of coinfirmed operons.
CONDOP-package
Develop ensemble classifiers for condition-dependent operon...
ct1
Coverage Vector 1
detect.sid.points
Find strat/end transcription points.
getCondOperonMap
Build the condition-dependent operon map for a given RNA-seq...
get.info
Get generic info about the door operons that have been...
get.intergenic.regions
Build a data table containing generic information on...
get.NCBI.seq
Find and get a genome sequence by specifyng the accession...
get.operon.end.points
Determine operon end-points (OEPs).
get.operon.start.points
Determine operon start-points (OSPs).
join.genes.and.operons
Join gene(s) and operon(s) annotations.
pred.operon.status
Predict operon status of gene pairs (e.g., POPs, DOPs,...).
pre.proc
Prepare data inputs for the main function 'run.CONDOP()'.
pre.processing
Normalize the data before the classification step.
qcut
Determine cutoff values for a given RNA-seq expression...
read.annot.from.gff
Read a GFF file from NCBI and return a GRanges object.
read.door.annotations
Read the operon(s) data file downloaded from...
read.gff.annotations
Read gene annotations in GFF format
remove.cov.depth.from.aFeat
Remove the read coverage on a given feature (e.g. rRNA and...
run.CONDOP
Build condition-dependent operon maps.
select.nops
Define a set of NOPs which is used to train the operon...
select.ops
Define a set of OPs which is used to train the operon...
select.ops.indoor
Define the set of OPs annotated in DOOR.
select.pops
Define a set of gene pairs POPs with an "operon status" to...
sum.conf.matrix
Provide classification metrics.
test.corr
Statistical test to find a putative transcription start (or...
train.RFs
Train and validate the operon classifier and evaluate the...
tune.cls
Tune and build the classification models.
validate.cls
Validate the classification models.

Files in this package

CONDOP
CONDOP/inst
CONDOP/inst/extdata
CONDOP/inst/extdata/1944.opr
CONDOP/inst/extdata/NC_000913.gff
CONDOP/NAMESPACE
CONDOP/data
CONDOP/data/datalist
CONDOP/data/ct1.rda
CONDOP/R
CONDOP/R/CONDOP.R
CONDOP/MD5
CONDOP/DESCRIPTION
CONDOP/man
CONDOP/man/comp.gene.transc.levels.Rd
CONDOP/man/qcut.Rd
CONDOP/man/select.nops.Rd
CONDOP/man/get.operon.start.points.Rd
CONDOP/man/pre.processing.Rd
CONDOP/man/ct1.Rd
CONDOP/man/get.NCBI.seq.Rd
CONDOP/man/train.RFs.Rd
CONDOP/man/read.door.annotations.Rd
CONDOP/man/tune.cls.Rd
CONDOP/man/CONDOP-package.Rd
CONDOP/man/get.intergenic.regions.Rd
CONDOP/man/select.ops.indoor.Rd
CONDOP/man/remove.cov.depth.from.aFeat.Rd
CONDOP/man/read.gff.annotations.Rd
CONDOP/man/comp.igr.transc.levels.Rd
CONDOP/man/sum.conf.matrix.Rd
CONDOP/man/get.operon.end.points.Rd
CONDOP/man/run.CONDOP.Rd
CONDOP/man/test.corr.Rd
CONDOP/man/read.annot.from.gff.Rd
CONDOP/man/validate.cls.Rd
CONDOP/man/join.genes.and.operons.Rd
CONDOP/man/select.ops.Rd
CONDOP/man/select.pops.Rd
CONDOP/man/compile.confirmed.operons.Rd
CONDOP/man/pred.operon.status.Rd
CONDOP/man/getCondOperonMap.Rd
CONDOP/man/get.info.Rd
CONDOP/man/detect.sid.points.Rd
CONDOP/man/pre.proc.Rd