Package index • devgru

Environment setup

kit_loadout(): Build the devgru environment by installing/loading packages
chrompar(): Scaffold function around easypar to run workflows in parallel by chromosome

read_bed_file(): Read in a BED file and convert to GenomicRanges or data.table
read_bedpe_file(): Read BEDPE File with Flexible Output Format
read_gtf_file(): Read in a GTF file and convert to GenomicRanges or data.table
read_maf_file(): Read MAF file and convert to GenomicRanges or data.table
read_vcf_file(): Read in a VCF file and convert to GenomicRanges or data.table

dt_to_gr(): Convert data.table to GenomicRanges Object
dt_to_gi(): Convert BEDPE-like data.table to GInteractions
gi_to_dt(): Convert GInteractions to BEDPE data.table format
gi_to_grl(): Convert GInteractions to GRangesList
grl_to_gi(): Convert GenomicRangesList to GInteractions
gr_to_seg(): Convert segmentation GenomicRanges object to a data.table with standardized columns and format

gr_flank(): Precise addition of flanking to GenomicRanges with boundary-aware options
gr_sanitycheck(): Check if input is a GenomicRanges object, plus optional sanity check of column names
dt_sanitycheck(): Check if input is a data.table object, plus optional sanity check of column names
gi_refactor_seqs(): Refactor seqinfo of GInteractions object for easy harmony
gr_refactor_seqs(): Refactor seqinfo, seqnames, seqlengths, seqlevels of GenomicRanges object for easy harmony
grl_refactor_seqs(): Refactor seqinfo of GRangesList object for easy harmony
aggregate_these(): Read and aggregate genomic or non-genomic data files with smart format detection

get_cbs_per_chromosome(): Single chromosome run circular binary segmentation (CBS) algorithm on read depth profile
get_corrected_cnv_profile(): Read in CNV profile data.table of various flavors and extract a corrected profile
get_cov_gap_imputation(): Generate gap imputed coverage from fragCounter output
get_deseq2_diff_expr(): Run DESeq2 differential expression analysis on RNA-seq count data
get_fgsea_pathway_enrichment(): Run fgsea gene set enrichment analysis on DESeq2 differential gene expression output
get_fragcounter_segmentation(): Generate a segmentation file from a fragCounter read depth profile
get_igh_trx_subtype(): Detect Canonical IGH Translocations in Multiple Myeloma
get_imputed_gaps_per_chromosome(): Single chromosome run imputation of small, NA read gaps in fragCounter coverage
get_jabba_qc_diagnostic(): Run diagnostic workflow of after JaBbA run to help evaluate quality of graph
get_maf_lite(): Convert SNV & InDel mutation table to MAF-lite format
get_maf_nonsynonymous(): Extract Non-Synonymous Mutations from MAF
get_protein_coding_genes(): Extract protein-coding genes from GTF file
get_qc_diagnostics_alignment(): Generate diagnostic plots for alignment QC checks using Alfred summary files
get_qc_diagnostics_snvindel(): Generate diagnostic plots for SNV & InDel variant calling QC checks
get_vaf(): Quick pull or explicitly calculate the VAF for mutation records of various flavors

geom_deseq2_volcano(): Volcano plot for exploring results from DESeq2 differential gene expression analysis
geom_gap_imputation(): Diagnostic plot used for reviewing the imputation of gaps in coverage profile
geom_gsea_enrichment(): Enrichment plot for exploring results from fgsea pathway enrichment analysis
geom_jabba_stats(): Diagnostic plot used for evaluating the performance of a JaBbA run
copynumber_palettier(): Create color palette for integer copy number states

cli_pio_colorscheme(): Set the color scheme options for pio CLI text in devgru
cli_stopwatch_end(): Verbose CLI output to designate a workflow end
cli_stopwatch_start(): Verbose CLI output to designate a workflow start
function_cli_intro(): Verbose CLI output for extended and rich description of steps along a complex workflow, typically used in a pipeline

braf_dnase_demo_dt_hg19: DNAaseI hypersensitivity sites for BRAF on hg19 as data.table
braf_dnase_demo_dt_hg38: DNAaseI hypersensitivity sites for BRAF on hg38 as data.table
chromosome_arms_hg38: Genomic coordinates of each chromosome arm on hg38 as GenomicRanges
example_dnase_hg38: DNAaseI hypersensitivity sites on hg38
exclusion_regions_hg38: Collection of genomic regions to exclude from analysis on hg38 as GenomicRanges
gene_body_hg38: Gene body segments from Ensemble v108 on hg38 as GenomicRanges
hmcl_conditions_demo_dt_hg38: Condition labels for associated RNA-seq counts matrix as data.table
hmcl_counts_demo_dt_hg38: RNA-seq counts matrix on hg38 as data.table
kras_dnase_demo_gr_hg19: DNAaseI hypersensitivity sites for KRAS on hg19 as GenomicRanges
kras_dnase_demo_gr_hg38: DNAaseI hypersensitivity sites for KRAS on hg38 as GenomicRanges
myeloma_translocation_ig_loci_hg38: Ig loci of recurrent translocations in multiple myeloma as GenomicRanges
myeloma_translocation_partner_loci_hg38: Partner loci of recurrent translocations in multiple myeloma as GenomicRanges
read_depth_demo_hg38: dryclean-fragCounter read depth profile on hg38 as GenomicRanges