Index

C

check_star_installed() (in module satay.fastq_to_bam)

count_insertions_over_intervals() (in module satay.process_satay_bams) create_genome_index() (in module satay.fastq_to_bam)

F

filter_bam() (in module satay.process_satay_bams) filter_insertions() (in module satay.process_satay_bams)

find_fastq_files() (in module satay.fastq_to_bam) find_paired_files() (in module satay.fastq_to_bam)

G

gene_da() (in module satay.da_analysis)

get_sample_name() (in module satay.fastq_to_bam)

L

load_filter_deseq() (in module satay.da_analysis)

M

main() (in module satay.cli) map_fastq_to_bam() (in module satay.fastq_to_bam) map_sample() (in module satay.process_satay_bams) merge_annotations() (in module satay.da_analysis) merge_bams() (in module satay.process_satay_bams) merge_cnts_files() (in module satay.process_satay_bams)

merge_files() (in module satay.process_satay_bams) module satay.cli satay.da_analysis satay.fastq_to_bam satay.process_satay_bams

P

process_orientation() (in module satay.process_satay_bams)

R

run_command() (in module satay.process_satay_bams)

run_deseq() (in module satay.da_analysis) run_star_alignment() (in module satay.fastq_to_bam)

S

satay.cli module satay.da_analysis module satay.fastq_to_bam module

satay.process_satay_bams module setup_logger() (in module satay.fastq_to_bam) setup_logging() (in module satay.process_satay_bams) sort_files() (in module satay.process_satay_bams)

V

validate_environment() (in module satay.process_satay_bams)

verify_star_index() (in module satay.fastq_to_bam)