Detect Annotation Releases and Repair Gene Names

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Documentation for package ‘genevintage’ version 0.1.3

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

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AggregateTranscripts	Sum transcript-level counts to gene level
aggregate_transcripts	Sum transcript-level counts to gene level
AnnotateGenes	Everything the annotation knows about a set of genes
annotate_genes	Everything the annotation knows about a set of genes
BuildSymbolIndex	Build a compact species/release gene-symbol index from GTF mappings
BuildSymbolIndexFromGTF	Fetch GTF mappings and build a symbol index
build_symbol_index	Build a compact species/release gene-symbol index from GTF mappings
build_symbol_index_from_gtf	Fetch GTF mappings and build a symbol index
CodingGenes	Protein-coding genes
coding_genes	Protein-coding genes
CompareReleases	Compare two releases of one annotation
compare_releases	Compare two releases of one annotation
CorrectGeneNames	Repair gene symbols a spreadsheet has converted to dates or numbers
correct_genenames	Repair gene symbols a spreadsheet has converted to dates or numbers
DetectRelease	Which Ensembl release a set of identifiers came from
DetectSpecies	Which species a set of identifiers belongs to
DetectSpeciesNames	Detect species from gene symbols
detect_release	Which Ensembl release a set of identifiers came from
detect_species	Which species a set of identifiers belongs to
detect_species_names	Detect species from gene symbols
EntrezIDs	NCBI Entrez identifiers for a set of genes
entrez_ids	NCBI Entrez identifiers for a set of genes
FetchMapping	Mapping table for one species and Ensembl release
FetchOrthologs	Ortholog table for one species pair and Ensembl release
FetchTranscripts	Transcript-to-gene table for one species and release
FetchXrefs	Ensembl gene identifiers and their cross-references, cached
fetch_mapping	Mapping table for one species and Ensembl release
fetch_orthologs	Ortholog table for one species pair and Ensembl release
fetch_transcripts	Transcript-to-gene table for one species and release
fetch_xrefs	Ensembl gene identifiers and their cross-references, cached
GeneBiotypes	What biotypes an annotation contains
GeneCache	Inspect or clear the download cache
GeneID2Name	Convert gene identifiers to gene names, detecting species and release
geneid2name	Convert gene identifiers to gene names, detecting species and release
GeneIDs	Gene identifiers for gene names or Entrez identifiers
GeneLengths	Exon-union gene lengths for one species and release
GeneNames	Convert gene identifiers to gene names
GenesByBiotype	Genes of a given biotype, or class of biotypes
genes_by_biotype	Genes of a given biotype, or class of biotypes
gene_biotypes	What biotypes an annotation contains
gene_cache	Inspect or clear the download cache
gene_ids	Gene identifiers for gene names or Entrez identifiers
gene_lengths	Exon-union gene lengths for one species and release
gene_names	Convert gene identifiers to gene names
GuessScheme	Which identifier scheme a vector of IDs uses
guess_scheme	Which identifier scheme a vector of IDs uses
HemoglobinGenes	Hemoglobin subunit genes
hemoglobin_genes	Hemoglobin subunit genes
lncRNAGenes	Long non-coding RNA genes
lncrna_genes	Long non-coding RNA genes
MHCGenes	Major histocompatibility complex genes
mhc_genes	Major histocompatibility complex genes
MitoGenes	Mitochondrial genes
mito_genes	Mitochondrial genes
NoncodingGenes	Non-coding RNA genes
noncoding_genes	Non-coding RNA genes
Orthologs	Find orthologs of gene identifiers in another species
orthologs	Find orthologs of gene identifiers in another species
OrthologSpecies	Species Compara publishes homologies for
ortholog_species	Species Compara publishes homologies for
ParseEns	Parse Ensembl identifiers into their parts
parse_ens	Parse Ensembl identifiers into their parts
QmaxViolations	Where the index violates its own ordering invariant
qmax_violations	Where the index violates its own ordering invariant
ResolveSpecies	Resolve a species name
resolve_species	Resolve a species name
RibosomalGenes	Ribosomal genes
ribosomal_genes	Ribosomal genes
rRNAGenes	Ribosomal RNA genes
rrna_genes	Ribosomal RNA genes
SexGenes	Sex-chromosome genes
sex_genes	Sex-chromosome genes
SpeciesTable	Species the index covers, with their common names
species_table	Species the index covers, with their common names
StreamExonLengths	Exon-union lengths from a GTF, streamed without writing it to disk
StreamGTF	Pull gene records out of a GTF without ever writing it to disk
StreamHomologies	Stream one species' orthologs against one other species
StreamTranscripts	Transcript-to-gene records from a GTF, streamed without writing it to disk
StreamXrefs	Stream one cross-reference TSV, keeping the gene-level pairs
stream_exon_lengths	Exon-union lengths from a GTF, streamed without writing it to disk
stream_gtf	Pull gene records out of a GTF without ever writing it to disk
stream_homologies	Stream one species' orthologs against one other species
stream_transcripts	Transcript-to-gene records from a GTF, streamed without writing it to disk
stream_xrefs	Stream one cross-reference TSV, keeping the gene-level pairs
Transcript2Gene	Map transcript identifiers to their genes
transcript2gene	Map transcript identifiers to their genes
tRNAGenes	Transfer RNA genes
trna_genes	Transfer RNA genes