Man pages for cobriniklab/cataRact
Functions for single cell work in the Cobrinik lab at CHLA

clean_gene_ediffClean Gene Ediff
clean_trs_ediffClean trs Ediff
color_by_gene_exprShade scatter plot by expression of marker genes
color_by_varquantifies mito read color_by_var(var_vect) \itemvar_vect A...
getGenefinds genename in ensemble<->gene association tables
helloHello, World!
karyo_obj-classA Karyo Object for use in plotting using the karyoploter...
load_dense_seg_datLoad Segmentation Objects Saved in a single .Rdata file
load_scattered_seg_datLoad Segmentation Objects saved in scattered individual...
lookup_genesLook Up Peak Genes on Segmentation Object
meetsConditionfunction that confirms genes meet expression conditions
parallel_scderun scde at the trs level for every comparison in a given...
plot_all_to_filePlot Segmentation Object across the whole Genome
plot_base_segPlot Segmentation on Karyoploter
plot_chrom_to_filePlot Segmentation Object across specific chromosomes
prep_for_karyoplotPrep for Karyoploter
prep_scde_inputPrep SCDE input
quantify_marker_exprQuantify Marker Expression
quantify_mitoQuantify Mitochondrial Expression
query_biomart_genesQuery BiomaRt Genes
query_biomart_transcriptsQuery BiomaRt Transcripts
RbindSegPlotConvert a list of segmentation objects output by copwriter...
refseq_from_trsidfunction that returns refseq gene symbols when given an...
run_gene_scderun scde at the gene level
run_trs_scderun scde at the transcript level
SingleSegPlotSingle Seg Plot
sort_T_b4_CLThis function sorts a list of granges objects sequenctially...
subset_jtfunction that subsets a matrix of feature counts...
tidy_lookup_genesTidy Look Up Genes
cobriniklab/cataRact documentation built on Jan. 9, 2018, 7:06 a.m.