Man pages for CONDOP
Condition-Dependent Operon Predictions
| 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. |
