Home
Fundamentals
User Guide
Contributing
Reference
Team
Components
Modules
Components
Workflows
Ingestion
BD Rhapsody
Cell Ranger mapping
Cell Ranger multi
Cell Ranger post-processing
Conversion
Demux
Make reference
Integration
Common
Harmony leiden
Initialize Integration
Initialize integration
Scanorama Leiden
Scanorama leiden
Scvi
Scvi
Multiomics
Full pipeline
Integration
Multisample
Prot multisample
Prot singlesample
Rna multisample
Rna singlesample
Integration
Bbknn leiden
Harmony leiden
Initialize integration
Leiden scvi
Scanorama leiden
Scvi leiden
Totalvi leiden
Qc
Qc
Modules
Annotate
Popv
Cluster
Leiden
Compression
Compress h5mu
Convert
From 10xh5 to h5mu
From 10xmtx to h5mu
From bd to 10x molecular barcode tags
From bdrhap to h5mu
From cellranger multi to h5mu
From h5ad to h5mu
From h5mu to h5ad
Velocyto to h5mu
Correction
Cellbender remove background
Cellbender remove background v0 2
Dataflow
Concat
Merge
Split modalities
Demux
Bcl convert
Bcl2fastq
Cellranger mkfastq
Dimred
Pca
Umap
Download
Download file
Sync test resources
Files
Make params
Filter
Delimit fraction
Do filter
Filter with counts
Filter with hvg
Filter with scrublet
Remove modality
Subset h5mu
Integrate
Harmonypy
Scanorama
Scarches
Scvi
Totalvi
Interpret
Lianapy
Labels Transfer
Knn
Xgboost
Mapping
BD Rhapsody
Cellranger count
Cellranger count split
Cellranger multi
Htseq count
Htseq count to h5mu
Multi star
Multi star to h5mu
Samtools sort
Star align
Star align v273a
Star build reference
Metadata
Add id
Grep annotation column
Join csv
Join uns to obs
Move obsm to obs
Neighbors
Bbknn
Find neighbors
Process 10xh5
Filter 10xh5
Qc
Calculate qc metrics
Fastqc
Multiqc
Query
Cellxgene census
Reference
Build bdrhap reference
Build cellranger reference
Make reference
Report
Mermaid
Transfer
Publish
Transform
Clr
Delete layer
Log1p
Normalize total
Regress out
Scale
Velocity
Scvelo
Velocyto
Modules