Index

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

omics_pipe AWS_installation Adding Modules Custom Pipeline about history installation license parameters pipelines tutorial 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)