Index

A | B | C | F | G | H | I | M | O | P | R | S | T

A

annotate_peaks() in module omics_pipe.modules.annotate_peaks, [1]
annotate_variants() in module omics_pipe.modules.annotate_variants

B

bowtie() in module omics_pipe.modules.bowtie, [1], [2]
BreastCancer_RNA_report() in module omics_pipe.modules.BreastCancer_RNA_report, [1], [2]
bwa1() in module omics_pipe.modules.bwa, [1], [2]
bwa2() in module omics_pipe.modules.bwa, [1], [2]
bwa_mem() in module omics_pipe.modules.bwa, [1], [2]
bwa_mem_pipe() in module omics_pipe.modules.bwa
bwa_RNA() in module omics_pipe.modules.bwa, [1], [2]

C

call_variants() in module omics_pipe.modules.call_variants
ChIP_trim() in module omics_pipe.modules.ChIP_trim, [1], [2]
cuffdiff() in module omics_pipe.modules.cuffdiff, [1], [2]
cuffdiff_miRNA() in module omics_pipe.modules.cuffdiff_miRNA
cufflinks() in module omics_pipe.modules.cufflinks, [1], [2]
cufflinks_miRNA() in module omics_pipe.modules.cufflinks_miRNA
cufflinks_ncRNA() in module omics_pipe.modules.cufflinks_ncRNA
cuffmerge() in module omics_pipe.modules.cuffmerge, [1], [2]
cuffmerge_miRNA() in module omics_pipe.modules.cuffmerge_miRNA
cuffmergetocompare() in module omics_pipe.modules.cuffmergetocompare, [1], [2]
cuffmergetocompare_miRNA() in module omics_pipe.modules.cuffmergetocompare_miRNA
custom_R_report() in module omics_pipe.modules.custom_R_report
cutadapt_miRNA() in module omics_pipe.modules.cutadapt_miRNA, [1], [2]

F

fastq_length_filter_miRNA() in module omics_pipe.modules.fastq_length_filter_miRNA, [1], [2]
fastqc() in module omics_pipe.modules.fastqc, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11]
fastqc_miRNA() in module omics_pipe.modules.fastqc_miRNA
filter_variants() in module omics_pipe.modules.filter_variants, [1], [2]
find_motifs() in module omics_pipe.modules.find_motifs, [1]
fusion_catcher() in module omics_pipe.modules.fusion_catcher, [1], [2]

G

GATK_preprocessing_WES() in module omics_pipe.modules.GATK_preprocessing_WES, [1]
GATK_preprocessing_WGS() in module omics_pipe.modules.GATK_preprocessing_WGS, [1]
GATK_variant_discovery() in module omics_pipe.modules.GATK_variant_discovery, [1]
GATK_variant_filtering() in module omics_pipe.modules.GATK_variant_filtering, [1]
GATK_variant_filtering_group() in module omics_pipe.modules.GATK_variant_filtering, [1]

H

homer_peaks() in module omics_pipe.modules.homer_peaks, [1]
htseq() in module omics_pipe.modules.htseq, [1], [2], [3], [4], [5]
htseq_gencode() in module omics_pipe.modules.htseq_gencode
htseq_miRNA() in module omics_pipe.modules.htseq_miRNA

I

intogen() in module omics_pipe.modules.intogen, [1], [2]

M

macs() in module omics_pipe.modules.macs, [1]
mutect() in module omics_pipe.modules.mutect, [1]

O

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omics_pipe.modules.annotate_peaks module, [1]
omics_pipe.modules.annotate_variants module
omics_pipe.modules.bowtie module, [1], [2]
omics_pipe.modules.BreastCancer_RNA_report module, [1], [2]
omics_pipe.modules.bwa module, [1], [2], [3], [4]
omics_pipe.modules.call_variants module
omics_pipe.modules.ChIP_trim module, [1], [2]
omics_pipe.modules.cuffdiff module, [1], [2]
omics_pipe.modules.cuffdiff_miRNA module
omics_pipe.modules.cufflinks module, [1], [2]
omics_pipe.modules.cufflinks_miRNA module
omics_pipe.modules.cufflinks_ncRNA module
omics_pipe.modules.cuffmerge module, [1], [2]
omics_pipe.modules.cuffmerge_miRNA module
omics_pipe.modules.cuffmergetocompare module, [1], [2]
omics_pipe.modules.cuffmergetocompare_miRNA module
omics_pipe.modules.custom_R_report module
omics_pipe.modules.cutadapt_miRNA module, [1], [2]
omics_pipe.modules.fastq_length_filter_miRNA module, [1], [2]
omics_pipe.modules.fastqc module, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11]
omics_pipe.modules.fastqc_miRNA module
omics_pipe.modules.filter_variants module, [1], [2]
omics_pipe.modules.find_motifs module, [1]
omics_pipe.modules.fusion_catcher module, [1], [2]
omics_pipe.modules.GATK_preprocessing_WES module, [1]
omics_pipe.modules.GATK_preprocessing_WGS module, [1]
omics_pipe.modules.GATK_variant_discovery module, [1]
omics_pipe.modules.GATK_variant_filtering module, [1]
omics_pipe.modules.homer_peaks module, [1]
omics_pipe.modules.htseq module, [1], [2], [3], [4], [5]
omics_pipe.modules.htseq_gencode module
omics_pipe.modules.htseq_miRNA module
omics_pipe.modules.intogen module, [1], [2]
omics_pipe.modules.macs module, [1]
omics_pipe.modules.mutect module, [1]
omics_pipe.modules.peak_track module, [1]
omics_pipe.modules.picard_mark_duplicates module, [1]
omics_pipe.modules.read_density module, [1]
omics_pipe.modules.RNAseq_QC module
omics_pipe.modules.RNAseq_report module
omics_pipe.modules.RNAseq_report_counts module, [1], [2], [3]
omics_pipe.modules.RNAseq_report_tuxedo module, [1], [2]
omics_pipe.modules.rseqc module, [1], [2]
omics_pipe.modules.snpir_variants module, [1], [2]
omics_pipe.modules.star module, [1], [2], [3], [4], [5]
omics_pipe.modules.star_piRNA module
omics_pipe.modules.TCGA_download module, [1], [2]
omics_pipe.modules.tophat module, [1], [2]
omics_pipe.modules.tophat_miRNA module
omics_pipe.modules.tophat_ncRNA module

P

peak_track() in module omics_pipe.modules.peak_track, [1]
picard_mark_duplicates() in module omics_pipe.modules.picard_mark_duplicates, [1]

R

read_density() in module omics_pipe.modules.read_density, [1]
RNAseq_QC() in module omics_pipe.modules.RNAseq_QC
RNAseq_report() in module omics_pipe.modules.RNAseq_report
RNAseq_report_counts() in module omics_pipe.modules.RNAseq_report_counts, [1], [2], [3]
RNAseq_report_tuxedo() in module omics_pipe.modules.RNAseq_report_tuxedo, [1], [2]
rseqc() in module omics_pipe.modules.rseqc, [1], [2]

S

snpir_variants() in module omics_pipe.modules.snpir_variants, [1], [2]
star() in module omics_pipe.modules.star, [1], [2], [3], [4], [5]
star_piRNA() in module omics_pipe.modules.star_piRNA

T

TCGA_download() in module omics_pipe.modules.TCGA_download, [1], [2]
tophat() in module omics_pipe.modules.tophat, [1], [2]
tophat_miRNA() in module omics_pipe.modules.tophat_miRNA
tophat_ncRNA() in module omics_pipe.modules.tophat_ncRNA