fastqcRun()
flexbarRun()
trim_galoreRun()
trimmomaticRun()
sortmernaRun()
STAR_Aligner
STAR_Aligner.build_index()
STAR_Aligner.check_index()
STAR_Aligner.run_Alignment()
hisat2_Aligner
hisat2_Aligner.build_index()
hisat2_Aligner.check_index()
hisat2_Aligner.run_Alignment()
align_stats()
featureCount()
htseqCount()
countMMG()
Normalization
Normalization.CPM()
Normalization.RPKM()
Normalization.TPM()
Normalization.meanRatioCount()
boxplot()
clusterSample()
leaf_label()
Gene_Description
Gene_Description.add_names()
Gene_Description.add_names_annotation()
degFilter()
runDESeq2()
run_edgeR()
GeneOntology
GeneOntology.barplotGO()
GeneOntology.dotplotGO()
GeneOntology.enrichGO()
Pathway
Pathway.barplotKEGG()
Pathway.dotplotKEGG()
Pathway.enrichKEGG()
PyseqrnaLogger()
add_MMG()
change_attribute()
change_ids()
check_files()
check_path()
check_status()
clusterRun()
findFiles()
getFiles()
getGenes()
get_basename()
get_cpu()
get_directory()
get_file_extension()
get_parent()
make_directory()
parse_config_file()
parse_gff()
read_input_file()
replace_cpu()
plotHeatmap()
plotMA()
plotVenn()
plotVolcano()
pyseqrna
pyseqrna.aligners
pyseqrna.arg_parser
pyseqrna.clustering
pyseqrna.differential_expression
pyseqrna.gene_ontology
pyseqrna.multimapped_groups
pyseqrna.normalize_counts
pyseqrna.pathway
pyseqrna.pyseqrna_plots
pyseqrna.pyseqrna_stats
pyseqrna.pyseqrna_utils
pyseqrna.quality_check
pyseqrna.quality_trimming
pyseqrna.quantification
pyseqrna.ribosomal
pyseqrna.version