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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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O
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P
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Q
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R
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S
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T
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U
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V
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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
alignmentSieve
Alleyoop collapse
Alleyoop rates
Alleyoop snpeval
Alleyoop summary
Alleyoop UTR Rates
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
Bamclipper
Bamliquidator
Bamplot
BaseQualityScoreRecalibrator
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
BEDPE file
Bedtools bamtobed
BioProcessTestCase (class in resolwe_bio.utils.test)
Bisulfite conversion rate
Bowtie (Dicty)
Bowtie genome index
Bowtie2
Bowtie2 genome index
BWA ALN
BWA genome index
BWA MEM
BWA SW
C
Cell Ranger Count
Cell Ranger Mkref
Chemical Mutagenesis
ChIP-Seq (Gene Score)
ChIP-seq (MACS2)
(MACS2-ROSE2)
ChIP-Seq (Peak Score)
ChipQC
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
Cut & Run
Cutadapt (3' mRNA-seq, single-end)
(Corall RNA-Seq, paired-end)
(Corall RNA-Seq, single-end)
(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
Deeptools bamCoverage
DESeq2
Detect library strandedness
Dictyostelium expressions
Differential Expression (table)
Differential expression of shRNA
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
Find similar genes
G
GAF file
GATK3 (HaplotypeCaller)
GATK4 (HaplotypeCaller)
Gene expression indices
Gene set
(create from Venn diagram)
(create)
GFF3 file
GO Enrichment analysis
GTF file
H
Hierarchical clustering of genes
Hierarchical clustering of samples
Hierarchical clustering of time courses
HISAT2
HISAT2 genome index
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
MACS2 - ROSE2
Mappability
Mappability info
MarkDuplicates
Merge Expressions (ETC)
Merge FASTQ (paired-end)
(single-end)
Metadata table for Orange
methcounts
miRNA pipeline
MultiQC
O
OBO file
P
PCA
Picard AlignmentSummary
Picard CollectRrbsMetrics
Picard CollectTargetedPcrMetrics
Picard InsertSizeMetrics
Picard WGS Metrics
Pre-peakcall QC
Prepare GEO - ChIP-Seq
Prepare GEO - RNA-Seq
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_paired_reads() (resolwe_bio.utils.test.BioProcessTestCase method)
prepare_reads() (resolwe_bio.utils.test.BioProcessTestCase method)
prepare_ref_seq() (resolwe_bio.utils.test.BioProcessTestCase method)
Q
QoRTs QC
Quantify shRNA species using bowtie2
R
Reads (QSEQ multiplexed, paired)
(QSEQ multiplexed, single)
(scRNA 10x)
resolwe_bio.utils (module)
resolwe_bio.utils.test (module)
Reverse complement FASTQ (paired-end)
(single-end)
RNA-Seq (Cuffquant)
ROSE2
RSEM
S
Salmon Index
Salmon Quant
SAM header
Samtools idxstats
Secondary hybrid BAM file
setUp() (resolwe_bio.utils.test.BioProcessTestCase method)
(resolwe_bio.utils.test.KBBioProcessTestCase method)
shRNA quantification
Single cell BAM file and index
skipDockerFailure() (in module resolwe_bio.utils.test)
skipUnlessLargeFiles() (in module resolwe_bio.utils.test)
Slam count
Slamdunk (paired-end)
snpEff
,
[1]
Spike-ins quality control
SRA data
(paired-end)
(single-end)
STAR
STAR genome index
Subsample FASTQ (paired-end)
(single-end)
Subsample FASTQ and BWA Aln (paired-end)
(single-end)
T
Test basic fields
Test disabled inputs
Test hidden inputs
Test select controler
Test sleep progress
Trim Galore (paired-end)
Trimmomatic (paired-end)
(single-end)
Trimmomatic - HISAT2 - HTSeq-count (paired-end)
(single-end)
U
UMI-tools dedup
Upload Picard CollectTargetedPcrMetrics
Upload proteomics sample
Upload proteomics sample set
V
Variant calling (CheMut)
Variant filtering (CheMut)
VCF file
W
WALT
WALT genome index
WGBS (paired-end)
(single-end)
WGS (paired-end) analysis
Whole exome sequencing (WES) analysis
Whole length Slamdunk analysis (paired-end)
Writing processes
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