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440 files changed
+1230
-1233
lines changed- .github/workflows
- target
- docker
- annotate/popv
- cluster/leiden
- compression
- compress_h5mu
- tar_extract
- 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
- from_h5mu_to_seurat
- velocyto_to_h5mu
- correction
- cellbender_remove_background_v0_2
- cellbender_remove_background
- dataflow
- concatenate_h5mu
- concat
- merge
- split_modalities
- demux
- bcl2fastq
- bcl_convert
- cellranger_mkfastq
- dimred
- pca
- tsne
- umap
- download
- download_file
- sync_test_resources
- feature_annotation
- highly_variable_features_scanpy
- score_genes_cell_cycle_scanpy
- score_genes_scanpy
- files/make_params
- filter
- delimit_fraction
- do_filter
- filter_with_counts
- filter_with_hvg
- filter_with_scrublet
- intersect_obs
- remove_modality
- subset_h5mu
- genetic_demux
- bcftools
- cellsnp
- demuxlet
- dsc_pileup
- freebayes
- freemuxlet
- samtools
- scsplit
- souporcell
- vireo
- integrate
- harmonypy
- scanorama
- scarches
- scvi
- totalvi
- interactive
- run_cellxgene
- run_cirrocumulus
- interpret/lianapy
- labels_transfer
- knn
- xgboost
- mapping
- bd_rhapsody
- cellranger_count_split
- cellranger_count
- cellranger_multi
- htseq_count_to_h5mu
- htseq_count
- multi_star_to_h5mu
- multi_star
- samtools_sort
- star_align_v273a
- star_align
- 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
- move_layer
- normalize_total
- regress_out
- scale
- velocity
- scvelo
- velocyto
- native
- compression
- compress_h5mu
- tar_extract
- dataflow
- concatenate_h5mu
- concat
- merge
- split_modalities
- download/sync_test_resources
- feature_annotation/score_genes_cell_cycle_scanpy
- integrate
- scarches
- totalvi
- labels_transfer
- knn
- xgboost
- metadata
- add_id
- grep_annotation_column
- transform/scale
- velocity
- scvelo
- velocyto
- nextflow
- 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
- from_h5mu_to_seurat
- velocyto_to_h5mu
- correction
- cellbender_remove_background_v0_2
- cellbender_remove_background
- dataflow
- concatenate_h5mu
- concat
- merge
- split_modalities
- demux
- bcl2fastq
- bcl_convert
- cellranger_mkfastq
- dimred
- pca
- tsne
- umap
- download
- download_file
- sync_test_resources
- feature_annotation/highly_variable_features_scanpy
- files/make_params
- filter
- delimit_fraction
- do_filter
- filter_with_counts
- filter_with_hvg
- filter_with_scrublet
- intersect_obs
- remove_modality
- subset_h5mu
- genetic_demux
- bcftools
- cellsnp
- demuxlet
- dsc_pileup
- freebayes
- freemuxlet
- samtools
- scsplit
- souporcell
- vireo
- integrate
- harmonypy
- scanorama
- scarches
- scvi
- totalvi
- interpret/lianapy
- labels_transfer
- knn
- xgboost
- mapping
- bd_rhapsody
- cellranger_count_split
- cellranger_count
- cellranger_multi
- htseq_count_to_h5mu
- htseq_count
- multi_star_to_h5mu
- multi_star
- samtools_sort
- star_align_v273a
- star_align
- 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
- move_layer
- normalize_total
- regress_out
- scale
- velocity
- scvelo
- velocyto
- workflows
- gdo/gdo_singlesample
- ingestion
- bd_rhapsody
- cellranger_mapping
- cellranger_multi
- cellranger_postprocessing
- conversion
- demux
- make_reference
- integration
- bbknn_leiden
- harmony_leiden
- scanorama_leiden
- scvi_leiden
- totalvi_leiden
- multiomics
- dimensionality_reduction
- process_batches
- process_samples
- split_modalities
- prot
- prot_multisample
- prot_singlesample
- qc/qc
- rna
- rna_multisample
- rna_singlesample
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