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resolwe-bio
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A
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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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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
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X
A
Abstract alignment process
Abstract annotation process
Abstract bed process
Abstract differential expression process
Abstract expression process
alignmentSieve
Annotate novel splice junctions (regtools)
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
BBDuk - STAR - featureCounts - QC
BED file
BEDPE file
Bedtools bamtobed
Beta Cut & Run workflow
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 MEM2
BWA SW
BWA-MEM2 genome index
BWA-MEM2 index files
C
Calculate coverage (bamCoverage)
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
Cuffdiff 2.2
Cufflinks 2.2
Cuffmerge
Cuffnorm
Cuffquant 2.2
Cuffquant results
Cut & Run
Cutadapt (3' mRNA-seq, single-end)
(Corall RNA-Seq, paired-end)
(Corall RNA-Seq, single-end)
(paired-end)
(single-end)
Cutadapt - STAR - StringTie (Corall, paired-end)
(Corall, single-end)
D
DESeq2
Detect library strandedness
Dictyostelium expressions
Differential Expression (table)
Differential expression of shRNA
E
edgeR
Ensembl Variant Effect Predictor
Ensembl-VEP cache directory
Expression aggregator
Expression matrix
Expression Time Course
Expression time course
F
FASTA file
FASTQ file (paired-end)
(single-end)
Find similar genes
G
GAF file
GATK filter variants (VQSR)
GATK GenomicsDBImport
GATK GenotypeGVCFs
GATK HaplotypeCaller (GVCF)
GATK MergeVcfs
GATK refine variants
GATK SelectVariants (multi-sample)
(single-sample)
GATK SplitNCigarReads
GATK VariantFiltration (multi-sample)
(single-sample)
GATK VariantsToTable
GATK4 (HaplotypeCaller)
Gene set
(create from Venn diagram)
(create)
GEO import
GFF3 file
GTF file
H
Hierarchical clustering of time courses
HISAT2
HISAT2 genome index
HMR
I
IDAT file
K
KBBioProcessTestCase (class in resolwe_bio.utils.test)
M
MACS 1.4
MACS 2.0
MACS2
MACS2 - ROSE2
Map microarray probes
Mappability
Mappability info
MarkDuplicates
Merge Expressions (ETC)
Merge FASTQ (paired-end)
(single-end)
Metadata table
(one-to-one)
methcounts
miRNA pipeline
ML-ready expression
module
resolwe_bio.utils
resolwe_bio.utils.test
MultiQC
O
OBO file
P
PCA
Picard AlignmentSummary
Picard CollectRrbsMetrics
Picard InsertSizeMetrics
Picard WGS Metrics
Pre-peakcall QC
Prepare GEO - ChIP-Seq
Prepare GEO - RNA-Seq
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
QuantSeq workflow
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)
RNA-seq variant calling preprocess
RNA-seq Variant Calling Workflow
RNA-SeQC
ROSE2
run_process() (resolwe_bio.utils.test.KBBioProcessTestCase method)
S
Salmon Index
SAM header
Samtools bedcov
Samtools coverage (multi-sample)
(single-sample)
Samtools fastq (paired-end)
Samtools idxstats
Samtools view
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)
snpEff (General variant annotation) (multi-sample)
(single-sample)
Spike-ins quality control
SRA data
(paired-end)
(single-end)
STAR
STAR genome index
STAR-based gene quantification workflow
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)
U
UMI-tools dedup
Upload microarray expression (unmapped)
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
WGS analysis (GVCF)
WGS preprocess data with bwa-mem2
Whole exome sequencing (WES) analysis
Writing processes
X
Xengsort classify
Xengsort index
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