biopipen.ns

package

biopipen.ns

</>

module

biopipen.ns.cellranger

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Cellranger pipeline module for BioPipen

Classes

CellRangerCount (Proc) — Run cellranger count</>
CellRangerVdj (Proc) — Run cellranger vdj</>
CellRangerSummary (Proc) — Summarize cellranger metrics</>

module

biopipen.ns.cnv

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CNV/CNA-related processes, mostly tertiary analysis

Classes

AneuploidyScore (Proc) — Chromosomal arm SCNA/aneuploidy</>
AneuploidyScoreSummary (Proc) — Summary table and plots from AneuploidyScore</>
TMADScore (Proc) — Trimmed Median Absolute Deviation (TMAD) score for CNV</>
TMADScoreSummary (Proc) — Summary table and plots for TMADScore</>

module

biopipen.ns.protein

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Protein-related processes.

Classes

Prodigy (Proc) — Prediction of binding affinity of protein-protein complexes based onintermolecular contacts using Prodigy. </>
ProdigySummary (Proc) — Summary of the output from Prodigy.</>

module

biopipen.ns.delim

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Tools to deal with csv/tsv files

Classes

RowsBinder (Proc) — Bind rows of input files</>
SampleInfo (Proc) — List sample information and perform statistics</>

module

biopipen.ns.plot

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Plotting data

Classes

VennDiagram (Proc) — Plot Venn diagram</>
Heatmap (Proc) — Plot heatmaps using ComplexHeatmap</>
ROC (Proc) — Plot ROC curve using plotROC.</>
Manhattan (Proc) — Plot Manhattan plot.</>
QQPlot (Proc) — Generate QQ-plot or PP-plot using qqplotr.</>
Scatter (Proc) — Generate scatter plot using ggplot2.</>

module

biopipen.ns.regulatory

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Provides processes for the regulatory related

Classes

MotifScan (Proc) — Scan the input sequences for binding sites using motifs.</>
MotifAffinityTest (Proc) — Test the affinity of motifs to the sequences and the affinity changedue the mutations. </>
VariantMotifPlot (Proc) — A plot with a genomic region surrounding a genomic variant, andpotentially disrupted motifs. </>

module

biopipen.ns.snp

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Plink processes

Classes

PlinkSimulation (Proc) — Simulate SNPs using PLINK v2</>
MatrixEQTL (Proc) — Run Matrix eQTL</>
PlinkFromVcf (Proc) — Convert VCF to PLINK format.</>
Plink2GTMat (Proc) — Convert PLINK files to genotype matrix.</>
PlinkIBD (Proc) — Run PLINK IBD analysis (identity by descent)</>
PlinkHWE (Proc) — Hardy-Weinberg Equilibrium report and filtering</>
PlinkHet (Proc) — Calculation of sample heterozygosity.</>
PlinkCallRate (Proc) — Calculation of call rate for the samples and variants.</>
PlinkFilter (Proc) — Filter samples and variants for PLINK files.</>
PlinkFreq (Proc) — Calculate allele frequencies for the variants.</>
PlinkUpdateName (Proc) — Update variant names in PLINK files.</>

module

biopipen.ns.bed

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Tools to handle BED files

Classes

BedLiftOver (Proc) — Liftover a BED file using liftOver</>
Bed2Vcf (Proc) — Convert a BED file to a valid VCF file with minimal information</>
BedConsensus (Proc) — Find consensus regions from multiple BED files.</>
BedtoolsMerge (Proc) — Merge overlapping intervals in a BED file, using bedtools merge</>
BedtoolsIntersect (Proc) — Find the intersection of two BED files, using bedtools intersect</>
BedtoolsMakeWindows (Proc) — Make windows from a BED file or genome size file, using bedtools makewindows.</>

module

biopipen.ns.tcgamaf

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Processes for TCGA MAF files.

Classes

Maf2Vcf (Proc) — Converts a MAF file to a VCF file.</>
MafAddChr (Proc) — Adds the chr prefix to chromosome names in a MAF file if not present.</>

module

biopipen.ns.cellranger_pipeline

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The cellranger pipelines

Primarily cellranger process plus summary for summarizing the metrics for multiple samples.

Classes

CellRangerCountPipeline — The cellranger count pipeline</>
CellRangerVdjPipeline — The cellranger vdj pipeline</>

module

biopipen.ns.scrna_metabolic_landscape

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Metabolic landscape analysis for scRNA-seq data

Classes

MetabolicPathwayActivity (Proc) — This process calculates the pathway activities in different groups and subsets.</>
MetabolicFeatures (Proc) — This process performs enrichment analysis for the metabolic pathwaysfor each group in each subset. </>
MetabolicFeaturesIntraSubset (Proc) — Intra-subset metabolic features - Enrichment analysis in details</>
MetabolicPathwayHeterogeneity (Proc) — Calculate Metabolic Pathway heterogeneity.</>
ScrnaMetabolicLandscape — Metabolic landscape analysis for scRNA-seq data</>

module

biopipen.ns.tcr

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Tools to analyze single-cell TCR sequencing data

Classes

ImmunarchLoading (Proc) — Immuarch - Loading data</>
ImmunarchFilter (Proc) — Immunarch - Filter data</>
Immunarch (Proc) — Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires</>
SampleDiversity (Proc) — Sample diversity and rarefaction analysis</>
CloneResidency (Proc) — Identification of clone residency</>
Immunarch2VDJtools (Proc) — Convert immuarch format into VDJtools input formats.</>
ImmunarchSplitIdents (Proc) — Split the data into multiple immunarch datasets by Idents from Seurat</>
VJUsage (Proc) — Circos-style V-J usage plot displaying the frequency ofvarious V-J junctions using vdjtools. </>
Attach2Seurat (Proc) — Attach the clonal information to a Seurat object as metadata</>
TCRClustering (Proc) — Cluster the TCR clones by their CDR3 sequences</>
TCRClusterStats (Proc) — Statistics of TCR clusters, generated by TCRClustering.</>
CloneSizeQQPlot (Proc) — QQ plot of the clone sizes</>
CDR3AAPhyschem (Proc) — CDR3 AA physicochemical feature analysis</>
TESSA (Proc) — Tessa is a Bayesian model to integrate T cell receptor (TCR) sequenceprofiling with transcriptomes of T cells. </>
TCRDock (Proc) — Using TCRDock to predict the structure of MHC-peptide-TCR complexes</>

module

biopipen.ns.cnvkit_pipeline

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The CNVkit pipeline.

Classes

CNVkitPipeline — The CNVkit pipeline</>

module

biopipen.ns.stats

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Provides processes for statistics.

Classes

ChowTest (Proc) — Massive Chow tests.</>
Mediation (Proc) — Mediation analysis.</>
LiquidAssoc (Proc) — Liquid association tests.</>
DiffCoexpr (Proc) — Differential co-expression analysis.</>
MetaPvalue (Proc) — Calulation of meta p-values.</>
MetaPvalue1 (Proc) — Calulation of meta p-values.</>

module

biopipen.ns.vcf

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Tools to handle VCF files

Classes

VcfLiftOver (Proc) — Liftover a VCF file using GATK</>
VcfFilter (Proc) — Filter records in vcf file</>
VcfIndex (Proc) — Index VCF files. If they are already index, use the index files</>
Vcf2Bed (Proc) — Convert Vcf file to Bed file</>
VcfDownSample (Proc) — Down-sample VCF files to keep only a subset of variants in there</>
VcfSplitSamples (Proc) — Split a VCF file into multiple VCF files, one for each sample</>
VcfIntersect (Proc) — Find variants in both VCF files</>
VcfFix (Proc) — Fix some issues with VCF files</>
VcfAnno (Proc) — Annotate a VCF file using vcfanno</>
TruvariBench (Proc) — Run truvari bench to compare a VCF with CNV calls andbase CNV standards </>
TruvariBenchSummary (Proc) — Summarise the statistics from TruvariBench for multiple jobs (VCFs)</>
TruvariConsistency (Proc) — Run truvari consistency to check consistency of CNV calls</>
BcftoolsAnnotate (Proc) — Add or remove annotations from VCF files</>
BcftoolsFilter (Proc) — Apply fixed threshold filters to VCF files</>
BcftoolsSort (Proc) — Sort VCF files using bcftools sort.</>
BcftoolsView (Proc) — View, subset and filter VCF files by position and filtering expression.</>

module

biopipen.ns.misc

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Misc processes

Classes

File2Proc (Proc) — Accept a file and pass it down with a symbolic link</>
Glob2Dir (Proc) — Create symbolic links in output directory for the files givenby the glob pattern </>
Config2File (Proc) — Write a configurationn in string to a configuration file</>
Str2File (Proc) — Write the given string to a file</>
Shell (Proc) — Run a shell command</>

module

biopipen.ns.gsea

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Gene set enrichment analysis

Classes

GSEA (Proc) — Gene set enrichment analysis</>
PreRank (Proc) — PreRank the genes for GSEA analysis</>
FGSEA (Proc) — Gene set enrichment analysis using fgsea</>
Enrichr (Proc) — Gene set enrichment analysis using Enrichr</>

module

biopipen.ns.gene

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Gene related processes

Classes

GeneNameConversion (Proc) — Convert gene names back and forth using MyGeneInfo</>
GenePromoters (Proc) — Get gene promoter regions by specifying the flanking regions of TSS</>

module

biopipen.ns.scrna

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Tools to analyze single-cell RNA

Classes

SeuratLoading (Proc) — Seurat - Loading data</>
SeuratPreparing (Proc) — Load, prepare and apply QC to data, using Seurat</>
SeuratClustering (Proc) — Determine the clusters of cells without reference using Seurat FindClustersprocedure. </>
SeuratSubClustering (Proc) — Find clusters of a subset of cells.</>
SeuratClusterStats (Proc) — Statistics of the clustering.</>
ModuleScoreCalculator (Proc) — Calculate the module scores for each cell</>
CellsDistribution (Proc) — Distribution of cells (i.e. in a TCR clone) from different groupsfor each cluster </>
SeuratMetadataMutater (Proc) — Mutate the metadata of the seurat object</>
DimPlots (Proc) — Seurat - Dimensional reduction plots</>
MarkersFinder (Proc) — Find markers between different groups of cells</>
TopExpressingGenes (Proc) — Find the top expressing genes in each cluster</>
ExprImputation (Proc) — This process imputes the dropout values in scRNA-seq data.</>
SCImpute (Proc) — Impute the dropout values in scRNA-seq data.</>
SeuratFilter (Proc) — Filtering cells from a seurat object</>
SeuratSubset (Proc) — Subset a seurat object into multiple seruat objects</>
SeuratSplit (Proc) — Split a seurat object into multiple seruat objects</>
Subset10X (Proc) — Subset 10X data, mostly used for testing</>
SeuratTo10X (Proc) — Write a Seurat object to 10X format</>
ScFGSEA (Proc) — Gene set enrichment analysis for cells in different groups using fgsea</>
CellTypeAnnotation (Proc) — Annotate the cell clusters. Currently, four ways are supported:</>
SeuratMap2Ref (Proc) — Map the seurat object to reference</>
RadarPlots (Proc) — Radar plots for cell proportion in different clusters.</>
MetaMarkers (Proc) — Find markers between three or more groups of cells, using one-way ANOVAor Kruskal-Wallis test. </>
Seurat2AnnData (Proc) — Convert seurat object to AnnData</>
AnnData2Seurat (Proc) — Convert AnnData to seurat object</>
ScSimulation (Proc) — Simulate single-cell data using splatter.</>
CellCellCommunication (Proc) — Cell-cell communication inference</>
CellCellCommunicationPlots (Proc) — Visualization for cell-cell communication inference.</>

module

biopipen.ns.bam

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Tools to process sam/bam/cram files

Classes

CNVpytor (Proc) — Detect CNV using CNVpytor</>
ControlFREEC (Proc) — Detect CNVs using Control-FREEC</>
CNAClinic (Proc) — Detect CNVs using CNAClinic</>
BamSplitChroms (Proc) — Split bam file by chromosomes</>
BamMerge (Proc) — Merge bam files</>
BamSampling (Proc) — Keeping only a fraction of read pairs from a bam file</>
BamSubsetByBed (Proc) — Subset bam file by the regions in a bed file</>

module

biopipen.ns.cnvkit

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CNVkit commnads

Classes

CNVkitAccess (Proc) — Calculate the sequence-accessible coordinates in chromosomes from thegiven reference genome using cnvkit.py access </>
CNVkitAutobin (Proc) — Quickly estimate read counts or depths in a BAM file to estimatereasonable on- and (if relevant) off-target bin sizes. </>
CNVkitCoverage (Proc) — Run cnvkit coverage</>
CNVkitReference (Proc) — Run cnvkit reference</>
CNVkitFix (Proc) — Run cnvkit.py fix</>
CNVkitSegment (Proc) — Run cnvkit.py segment</>
CNVkitScatter (Proc) — Run cnvkit.py scatter</>
CNVkitDiagram (Proc) — Run cnvkit.py diagram</>
CNVkitHeatmap (Proc) — Run cnvkit.py heatmap for multiple cases</>
CNVkitCall (Proc) — Run cnvkit.py call</>
CNVkitBatch (Proc) — Run cnvkit batch</>
CNVkitGuessBaits (Proc) — Guess the bait intervals from the bam files</>

module

biopipen.ns.web

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Get data from the web

Classes

Download (Proc) — Download data from URLs</>
DownloadList (Proc) — Download data from URLs in a file.</>
GCloudStorageDownloadFile (Proc) — Download file from Google Cloud Storage</>
GCloudStorageDownloadBucket (Proc) — Download all files from a Google Cloud Storage bucket</>

module

biopipen.ns.rnaseq

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RNA-seq data analysis

Classes

UnitConversion (Proc) — Convert expression value units back and forth</>
Simulation (Proc) — Simulate RNA-seq data using ESCO/RUVcorr package</>