resolwe-bio
readthedocs-dependencies
Writing processes
Process catalog
Descriptor schemas
Reference
Change Log
Contributing
resolwe-bio
Docs
»
Index
Edit on GitHub
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
K
|
L
|
M
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
A
Abstract alignment process
Abstract annotation process
Abstract bed process
Abstract differential expression process
Abstract expression process
Accel Amplicon Pipeline
Align (BWA) and trim adapters
Amplicon report
Amplicon table
Annotate novel splice junctions (regtools)
Archive and make multi-sample report for amplicon data
Archive samples
ATAC-Seq
B
BAM file
BAM file and index
Bam split
Bamliquidator
Bamplot
BaseSpace file
BBDuk (paired-end)
(single-end)
BBDuk - Salmon - QC (paired-end)
(single-end)
BBDuk - STAR - FeatureCounts (3' mRNA-Seq, paired-end)
(3' mRNA-Seq, single-end)
BBDuk - STAR - featureCounts - QC (paired-end)
(single-end)
BBDuk - STAR - HTSeq-count (paired-end)
(single-end)
BED file
BioProcessTestCase (class in resolwe_bio.utils.test)
Bowtie (Dicty)
Bowtie2
BWA ALN
BWA MEM
BWA SW
C
Chemical Mutagenesis
ChIP-Seq (Gene Score)
ChIP-seq (MACS2)
(MACS2-ROSE2)
ChIP-Seq (Peak Score)
Convert files to reads (paired-end)
(single-end)
Convert GFF3 to GTF
coverageBed
Cuffdiff 2.2
Cufflinks 2.2
Cuffmerge
Cuffnorm
Cuffquant 2.2
Cuffquant results
Custom master file
Cutadapt (Diagenode CATS, paired-end)
(Diagenode CATS, single-end)
(paired-end)
(single-end)
Cutadapt - STAR - FeatureCounts (3' mRNA-Seq, single-end)
Cutadapt - STAR - FeatureCounts - basic QC (3' mRNA-Seq, single-end)
Cutadapt - STAR - HTSeq-count (paired-end)
(single-end)
Cutadapt - STAR - RSEM (Diagenode CATS, paired-end)
(Diagenode CATS, single-end)
Cutadapt - STAR - StringTie (Corall, paired-end)
(Corall, single-end)
D
DESeq2
Detect library strandedness
Dictyostelium expressions
Differential Expression (table)
E
edgeR
Expression aggregator
Expression data
(Cuffnorm)
(STAR)
Expression matrix
Expression Time Course
Expression time course
F
FASTA file
FASTQ file (paired-end)
(single-end)
featureCounts
G
GAF file
GATK3 (HaplotypeCaller)
GATK4 (HaplotypeCaller)
Gene expression indices
Gene set
(create from Venn diagram)
(create)
Genome
GFF3 file
GO Enrichment analysis
GTF file
H
Hierarchical clustering of genes
Hierarchical clustering of samples
HISAT2
HMR
HTSeq-count (CPM)
(TPM)
I
Indel Realignment and Base Recalibration
K
KBBioProcessTestCase (class in resolwe_bio.utils.test)
L
LoFreq (call)
M
MACS 1.4
MACS 2.0
MACS2 - ROSE2
Mappability
Mappability info
Merge Expressions (ETC)
Metabolic pathway file
methcounts
miRNA pipeline
MultiQC
O
OBO file
P
PCA
Picard CollectTargetedPcrMetrics
Pre-peakcall QC
Prepare GEO - ChIP-Seq
Prepare GEO - RNA-Seq
prepare_adapters() (resolwe_bio.utils.test.BioProcessTestCase method)
prepare_amplicon_master_file() (resolwe_bio.utils.test.BioProcessTestCase method)
prepare_annotation() (resolwe_bio.utils.test.BioProcessTestCase method)
prepare_annotation_gff() (resolwe_bio.utils.test.BioProcessTestCase method)
prepare_bam() (resolwe_bio.utils.test.BioProcessTestCase method)
prepare_expression() (resolwe_bio.utils.test.BioProcessTestCase method)
prepare_genome() (resolwe_bio.utils.test.BioProcessTestCase method)
prepare_paired_reads() (resolwe_bio.utils.test.BioProcessTestCase method)
prepare_reads() (resolwe_bio.utils.test.BioProcessTestCase method)
Q
Quantify shRNA species using bowtie2
R
Reads (QSEQ multiplexed, paired)
(QSEQ multiplexed, single)
resolwe_bio.utils (module)
resolwe_bio.utils.test (module)
RNA-Seq (Cuffquant)
ROSE2
RSEM
S
Salmon Index
SAM header
Secondary hybrid BAM file
setUp() (resolwe_bio.utils.test.BioProcessTestCase method)
(resolwe_bio.utils.test.KBBioProcessTestCase method)
shRNA quantification
skipDockerFailure() (in module resolwe_bio.utils.test)
skipUnlessLargeFiles() (in module resolwe_bio.utils.test)
Slamdunk analysis (paired-end)
snpEff
,
[1]
Spike-ins quality control
SRA data
(paired-end)
(single-end)
STAR
STAR genome index
Subread
Subsample FASTQ (paired-end)
(single-end)
T
Test basic fields
Test disabled inputs
Test hidden inputs
Test select controler
Test sleep progress
Trimmomatic (paired-end)
(single-end)
Trimmomatic - HISAT2 - HTSeq-count (paired-end)
(single-end)
U
Upload Picard CollectTargetedPcrMetrics
V
Variant calling (CheMut)
Variant filtering (CheMut)
VCF file
W
WALT
WGBS
Whole exome sequencing (WES) analysis
Writing processes
Read the Docs
v: readthedocs-dependencies
Versions
latest
stable
trigger-build
readthedocs-dependencies
Downloads
pdf
html
epub
On Read the Docs
Project Home
Builds
Free document hosting provided by
Read the Docs
.