Index

A

alignmentSummaryMetrics() (in module txseq.pipeline_bamqc)

B

buildFastQCSummaryStatus() (in module txseq.pipeline_fastqc)

C

check_values() (in module txseq.tasks.samples) collectRnaSeqMetrics() (in module txseq.pipeline_bamqc)

contigs() (in module txseq.pipeline_ensembl) count() (in module txseq.pipeline_feature_counts) cutadapt() (in module txseq.pipeline_preprocess_quantseq_fwd)

E

estimateLibraryComplexity() (in module txseq.pipeline_bamqc)

exons() (in module txseq.pipeline_hisat_index) extractYPAR() (in module txseq.pipeline_ensembl)

F

filteredGTF() (in module txseq.pipeline_ensembl) filteredTranscriptFasta() (in module txseq.pipeline_ensembl) firstPass() (in module txseq.pipeline_hisat) flatGeneset() (in module txseq.pipeline_bamqc)

fractionSpliced() (in module txseq.pipeline_bamqc) full() (in module txseq.pipeline_ensembl) (in module txseq.pipeline_hisat_index) (in module txseq.pipeline_salmon_index)

G

geneCounts() (in module txseq.pipeline_feature_counts)

get_parameter_file() (in module txseq.tasks.parameters)

H

hardMaskYPAR() (in module txseq.pipeline_ensembl)

I

index() (in module txseq.pipeline_salmon_index) indir (txseq.tasks.setup.setup attribute)

inname (txseq.tasks.setup.setup attribute) insertSizeMetricsAndHistograms() (in module txseq.pipeline_bamqc) is_tool() (in module txseq.tasks.profile)

J

job_memory (txseq.tasks.setup.setup attribute)

job_threads (txseq.tasks.setup.setup attribute)

L

loadAlignmentSummaryMetrics() (in module txseq.pipeline_bamqc) loadCollectRnaSeqMetrics() (in module txseq.pipeline_bamqc) loadCounts() (in module txseq.pipeline_feature_counts) loadEstimateLibraryComplexity() (in module txseq.pipeline_bamqc) loadFastQC() (in module txseq.pipeline_fastqc) loadFractionSpliced() (in module txseq.pipeline_bamqc) loadGeneCounts() (in module txseq.pipeline_feature_counts) loadInsertSizeHistograms() (in module txseq.pipeline_bamqc) loadInsertSizeMetrics() (in module txseq.pipeline_bamqc) loadMetadata() (in module txseq.pipeline_fastqc)

loadNGenesDetected() (in module txseq.pipeline_feature_counts) loadNumberGenesDetected() (in module txseq.pipeline_salmon) loadQCSummary() (in module txseq.pipeline_bamqc) loadSalmonGeneQuant() (in module txseq.pipeline_salmon) loadSalmonTPMs() (in module txseq.pipeline_salmon) loadSalmonTranscriptQuant() (in module txseq.pipeline_salmon) loadSampleInformation() (in module txseq.pipeline_bamqc) loadThreePrimeBias() (in module txseq.pipeline_bamqc) loadTranscriptInfo() (in module txseq.pipeline_feature_counts) (in module txseq.pipeline_salmon) log_file (txseq.tasks.setup.setup attribute)

M

module txseq.pipeline_bamqc txseq.pipeline_ensembl txseq.pipeline_fastqc txseq.pipeline_feature_counts txseq.pipeline_hisat txseq.pipeline_hisat_index txseq.pipeline_preprocess_quantseq_fwd txseq.pipeline_salmon txseq.pipeline_salmon_index txseq.tasks.parameters txseq.tasks.profile txseq.tasks.samples txseq.tasks.setup

N

nGenesDetected() (in module txseq.pipeline_feature_counts)

novelSpliceSites() (in module txseq.pipeline_hisat) numberGenesDetected() (in module txseq.pipeline_salmon)

O

outdir (txseq.tasks.setup.setup attribute)

outname (txseq.tasks.setup.setup attribute)

P

parse_mem() (txseq.tasks.setup.setup method)

Q

qc() (in module txseq.pipeline_bamqc) qcSummary() (in module txseq.pipeline_bamqc)

quant() (in module txseq.pipeline_salmon) quantitation() (in module txseq.pipeline_salmon)

R

resources (txseq.tasks.setup.setup attribute)

S

salmonTPMs() (in module txseq.pipeline_salmon) sample (class in txseq.tasks.samples) samples (class in txseq.tasks.samples) secondPass() (in module txseq.pipeline_hisat)

set_resources() (txseq.tasks.setup.setup method) setup (class in txseq.tasks.setup) show() (txseq.tasks.samples.sample method) spliceSites() (in module txseq.pipeline_hisat_index)

T

threePrimeBias() (in module txseq.pipeline_bamqc) transcriptInfo() (in module txseq.pipeline_ensembl) transcriptomeIndex() (in module txseq.pipeline_hisat_index) transcriptToGeneMap() (in module txseq.pipeline_ensembl) tximeta() (in module txseq.pipeline_salmon) txseq.pipeline_bamqc module txseq.pipeline_ensembl module txseq.pipeline_fastqc module txseq.pipeline_feature_counts module txseq.pipeline_hisat module

txseq.pipeline_hisat_index module txseq.pipeline_preprocess_quantseq_fwd module txseq.pipeline_salmon module txseq.pipeline_salmon_index module txseq.tasks.parameters module txseq.tasks.profile module txseq.tasks.samples module txseq.tasks.setup module

W

write_config_files() (in module txseq.tasks.parameters)