Man pages for harshsharma-cb/FASE
Analysis of RNA-Sequencing data using FASE (Finding Alternative Splicing Events).
| addAnnotationDEG | Annotation of differentially expressed genes |
| addAnnotationDEJ | Annotation of differentially expressed junctions |
| addAnnotationRnaSeq | Add annotation to EP/IP events |
| connected.exons.igraph | Connected Exons using igraph |
| countMatrixGenes | Count Matrix Genes |
| cpmCountsDEG | cpmCountsDEG |
| cpmCountsDEJ | cpmCountsDEJ |
| cpmCountsEP | cpmCountsEP |
| DEG | Differentially Expressed Genes |
| DEJ | Differentially Expressed Junctions |
| dot-cmm | Title |
| dot-correctJunctionCoordinate | correctJunctionCoordinate |
| dot-epip.exp | Prepare files for hs and simscore |
| dot-ePrnaseqFunction | EP function |
| dot-extractIntrons | extractIntrons |
| dot-fitEPrnaseqModel | EP model fitting |
| dot-fitiPrnaseqModel | fitiPrnaseqModel |
| dot-getEIJcounts | .getEIJcounts |
| dot-getNumericCount | .getNumericCount |
| dot-Gstructure | Gene structure |
| dot-iPrnaseqFunction | iPrnaseqFunction |
| dot-iStructure | intron Structure |
| dot-prepareCounts | Prepare counts for ExonPointer and IntronPointer |
| dot-propagation | Transcript Structure: seed propagation function |
| dot-r.a.bias | Removing algebraic bias |
| dot-r.dup.ts | Removing duplicate transcript |
| dot-removeLECounts | Remove low-expressed reads |
| dot-removeLECountsTS | Title |
| dot-seed.exon.ep.excl | Title |
| dot-seed.exon.ep.incl | Seed exons |
| dot-seed.exon.ip.excl | Title |
| dot-s.exon.ip.incl | Title |
| dot-sumPvalsMethod | Sum of p-values |
| dot-transtruct.prep | Transtruct preparation function |
| EPrnaseq | ExonPointer |
| FASE | FASE: Finding Alternative Splicing Events (0.1.24) |
| getJunctionCountMatrix | Generate junction count matrix |
| getPvaluesByContrast | Cassette exon/intron retention event ranking by contrast |
| GTFnomencJunctionM | Junction Matrix Annotation |
| heatscore | Heatscore using Splice Index. |
| intronGTFparser | intronGTFparser |
| intronMembershipMatrix | Intron Membership Matrix |
| iPrnaseq | Intron Pointer |
| JunctionMatrixAnnotation | Junction Matrix Annotation |
| ppAuto | RNA Seq and Alternative Splicing preprocessing function |
| ppFASE | Alternative Splicing Pre-processing |
| ppRawData | RNA Sequencing raw data preprocessing |
| ppSumEIG | RNA Seq Preprocessing Read Summarization |
| readMembershipMatrix | Read Membership Matrix |
| simscore | Similarity Score for network edge weight |
| survFASE | Survival analysis using metafeatures |
| transconc | Transcript Concentration |
| transtruct | Transcript Stucture |
