Man pages for jeremymcrae/publishedDeNovos
Published De Novos Dataset from Developmental Disorder Sequencing Studies

autism_de_novosget de novo data from autism exome studies
cohortsCohort information.
deligt_de_novosget de novo data for De Ligt et al. intellectual disability...
de_rubeis_de_novosget de novo data from the 2014 De Rubeis et al. autism exome...
epi4k_de_novosget de novo data for the Epi4K epilepsy exome study
find_matching_sitesthis identifies variants which match the current row
find_most_severe_transcriptfind the most severe transcript from Ensembl data
fix_coordinatesextract genomic coordinates for variants from a dataframe
fix_coordinates_with_alleleextract genomic coordinates for variants from a dataframe
fix_coordinates_with_hgvs_genomicextract genomic coordinates for variants encoded as HGVS...
fix_del_allelesfix deletion allele codes
fix_dup_allelesfix duplication allele codes
fix_het_allelescorrect alt alleles which have been encoded as an IUPAC...
fix_ins_allelesfix insertion allele codes
fix_sub_allelesfix substitution allele codes
fix_zaiidi_coordinatesextract genomic coordinates for variants from a dataframe
fromer_de_novosget de novo data from Fromer et al. schizophrenia exome study
get_deligt_denovo_tableload the supplementary table for the de ligt de novo variants
get_deligt_sexload the supplementary table for the de ligt sex information
get_deligt_textload the supplementary data for the de ligt de novos
get_gene_id_for_variantfind the hgnc symbol overlapping a variant position
get_protein_lengthfind the coding length for a ensembl transcript
get_sequence_in_regionfind genomic sequence within a region
get_vep_consequencefind the VEP consequence for a variant
gilissen_de_novosget de novo data for Gilissen et al. intellectual disability...
iossifov_nature_de_novosget de novo data from the 2014 Iossifov et al. autism exome...
iossifov_neuron_de_novosget de novo data from the 2012 Iossifov et al autism exome...
lelieveld_de_novosget de novo data for Lelieveld et al. intellectual disability...
map_coordinatesmap coordiantes from one assembly to another
oroak_de_novosget de novo data from the O'Roak et al autism exome study
rauch_de_novosget de novo data for Rauch et al. intellectual disability...
remove_duplicatesremove duplicate variants from the same individual
request_from_ensemblmake a URL request to the Ensembl service
sanders_de_novosget de novo data from the Sanders et al autism exome study
variantsDe novos from published studies.
zaidi_de_novosget de novo data from Zaidi et al. congenital heart disease...
jeremymcrae/publishedDeNovos documentation built on May 18, 2018, 8:24 p.m.