Man pages for drmjc/genomics
Genomics related functions.
| accession2chr | Change the GENOMEacc from gene2refseq into a chromosome name |
| alignment2ucsc | Convert an alignment to a ucsc location. |
| genomics-package | Genomics package. currently undocumented |
| get.taxonID | get.taxonID |
| import.gene2accession | import.gene2accession |
| import.gene2refseq | import a local copy of the gene2refseq file. |
| import.gene_info | import a local copy of the gene_info file. |
| import.gene.summary | import gene.summary file |
| import.gff | Import a GFF file |
| import.kgXref | import the kgXref file downloaded manually from UCSC genome... |
| import.knowngene | import the knownGene file downloaded manually from UCSC... |
| import.knownGene2gene | Download knownGeneToLocusLink from UCSC Table Browser to:... |
| import.miRbase | Import miRBase records. From the miRBase FTP site ([1]),... |
| import.mirbase.dropped | Import the miRNA.dead file Import the miRNA.dead file, and... |
| import.miRbase.locations | Import the genomic locations of the miRBase precursor... |
| import.miRbase.mir2miR | import.miRbase.miR2mir |
| import.miRbase.mirome | import.miRbase.miRome |
| import.ncbi.file | import.ncbi.file |
| import.ucsc.file | import UCSC-style file |
| import.unigene2gene | Import the gene2unigene file. |
| import.unigene.data | Import the Mm.data.gz file file. |
| int2char | Convert integers to characters |
| is.ucsc.string | is a UCSC string? |
| linkout.gene | Generate a weblink for a given Entrez GeneID to the Entrez... |
| linkout.ucsc | generate a weblink for a given Entrez GeneID to the UCSC... |
| make.gene.summary | Make an Entrez Gene Summary table which includes the genes... |
| make.ucsc.string | Convert an alignment to a ucsc location. |
| make.unique.gene2accession | find a unique genomic mapping for each entrez gene (if known) |
| make.unique.gene2refseq | find a unique genomic mapping for each entrez gene (if known) |
| mir2miR | Convert mature miR ID's into the immature, precursor form. |
| miRbase.miR2mir | Convert mirbase database Convert the miRbase db (which has... |
| mirbase.to.3p.5p | Convert miR ID's to 3p/5p The miRNA.xls file from miRbase... |
| mirIDsplit | Split the parts of a miRanda miRNA ID into the constituent... |
| miRNA.align.mir.to.miR | Align miR to mir sequences Sequence based alignment of mature... |
| miRNA.fix.miR.ids | Fix the names of microRNA's |
| mirna.pre2mature | Convert pre to mature microRNA's Convert a list of precursor... |
| miRNA.validate.miR.ID | Validate miR ID's |
| miRNA.which.arm | Predict miRNA arm Predict which arm (3' or 5') of the... |
| mirorder | Ordering permutation of mirbase ID's Get the index that each... |
| mirsort | Sort a vector of mirbase ID's |
| mirsplit | Split the parts of a mirana miRNA ID into the consituent... |
| miRuniverse | Obtain the miR universe What are the known miR's in a given... |
| order.refseq | order RefSeq ID's by validation status |
| range_merge_markers | merge a range of markers |
| rank.refseq | rank RefSeq identifiers |
| rename.gnf.markers | rename.gnf.markers |
| retrieve.genomic.loc | retrieve.genomic.loc |
| summarise.genomescan | summarise.genomescan |
| ucsc.pos | Convert an alignment to a ucsc location. |
| ucsc.pos2genoMb.pos | chromosome position to genome position Useful for Manhattan... |
| ucsc.pos.add | ucsc.pos.add |
| ucsc.pos.diff | Method to determine the distance between two genomic regions... |
| ucsc.pos.split | ucsc.pos.split |
| ucsc.pos.subset | ucsc.pos.subset |
| ucsc.size | interval sizes |
| ucsc.union | union of 2 genomic intervals |
| ucsc.unionN | union of multiple genomic intervals |
| write.expression.data | write.expression.data |
| write.fasta | write a FastA file |
