Index

A

alignment() (in module baseq.snv.gatk)

APA_usage() (in module baseq.drops.apa.samples), [1]

B

BAMTYPE (class in baseq.bam) baseq.align.bowtie2 (module) baseq.cnv (module) baseq.cnv.bincount (module) baseq.cnv.normalize (module) baseq.cnv.plots.genome (module) baseq.cnv.plots.region (module) baseq.cnv.segment (module) baseq.drops (module) baseq.drops.barcode.count (module) baseq.drops.barcode.split (module) baseq.drops.barcode.stats (module)

baseq.drops.run_star (module) baseq.drops.tag_gene (module) baseq.drops.whitelist (module) baseq.fastq.quality (module) baseq.fastq.sample_file (module) baseq.fastq.split_barcode (module) baseq.snv.gatk (module) baseq.snv.qc.enrich (module) baseq.snv.vcf.GATK (module) baseq.utils.runcommand (module) bowtie2_sort() (in module baseq.align.bowtie2) bqsr() (in module baseq.snv.gatk)

C

CBS() (in module baseq.cnv.segment) check_sample_files() (in module baseq.fastq.sample_file)

count_barcodes() (in module baseq.drops.barcode.count) counting() (in module baseq.cnv.bincount) create_pon() (in module baseq.snv.gatk)

E

extract_barcode() (in module baseq.drops.barcode.count)

G

get_columns() (baseq.bam.BAMTYPE method)

get_reads() (baseq.bam.BAMTYPE method) getUMI() (in module baseq.drops.barcode.split)

L

list_fastq_files() (in module baseq.fastq.sample_file)

M

mutect2() (in module baseq.snv.gatk)

N

normalize() (in module baseq.cnv.normalize)

P

plot_genome() (in module baseq.cnv.plots.genome)

plot_genome_multiple() (in module baseq.cnv.plots.genome) plot_region() (in module baseq.cnv.plots.region)

Q

quality() (in module baseq.fastq.quality)

quality_control() (in module baseq.snv.qc.enrich)

R

read_counts() (baseq.bam.BAMTYPE method) read_whitelist() (in module baseq.drops.whitelist) region_bed_depth() (baseq.bam.BAMTYPE method) region_depth() (baseq.bam.BAMTYPE method)

run_callvar() (in module baseq.snv.gatk) run_generator() (in module baseq.utils.runcommand) run_it() (in module baseq.utils.runcommand) run_markdup() (in module baseq.snv.gatk) run_multiple() (in module baseq.drops.run_star)

S

scan() (in module baseq.drops.apa.scaner) scan_genes() (in module baseq.drops.apa.genes) scan_utr() (in module baseq.drops.apa.UTR) selectvar() (in module baseq.snv.gatk) split() (in module baseq.drops.barcode.split)

split_barcode() (in module baseq.fastq.split_barcode) stats_bam() (baseq.bam.BAMTYPE method) stats_bases() (baseq.bam.BAMTYPE method) stats_duplicates() (baseq.bam.BAMTYPE method) stats_region_coverage() (baseq.bam.BAMTYPE method)

T

tagging_reads() (in module baseq.drops.tag_gene)

V

valid_barcode() (in module baseq.drops.barcode.stats)

vcf_stats() (in module baseq.snv.vcf.GATK)

W

whitelist_check() (in module baseq.drops.whitelist)