CONDOP: Condition-Dependent Operon Predictions

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.

AuthorVittorio Fortino <vittorio.fortino@ttl.fi>
Date of publication2016-02-24 15:47:51
MaintainerVittorio Fortino <vittorio.fortino@ttl.fi>
LicenseGPL-3
Version1.0

View on CRAN

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.

Functions

comp.gene.transc.levels Man page
comp.igr.transc.levels Man page
compile.confirmed.operons Man page
CONDOP Man page
CONDOP-package Man page
ct1 Man page
detect.sid.points Man page
getCondOperonMap Man page
get.info Man page
get.intergenic.regions Man page
get.NCBI.seq Man page
get.operon.end.points Man page
get.operon.start.points Man page
join.genes.and.operons Man page
pred.operon.status Man page
pre.proc Man page
pre.processing Man page
qcut Man page
read.annot.from.gff Man page
read.door.annotations Man page
read.gff.annotations Man page
remove.cov.depth.from.aFeat Man page
run.CONDOP Man page
select.nops Man page
select.ops Man page
select.ops.indoor Man page
select.pops Man page
sum.conf.matrix Man page
test.corr Man page
train.RFs Man page
tune.cls Man page
validate.cls Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.