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525 files changed
+1456
-1456
lines changed- target
- executable
- annotate
- celltypist
- onclass
- popv
- random_forest_annotation
- scanvi
- svm_annotation
- 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_h5ad_to_seurat
- from_h5mu_to_h5ad
- from_h5mu_to_seurat
- velocyto_to_h5mu
- correction
- cellbender_remove_background_v0_2
- cellbender_remove_background
- dataflow
- concatenate_h5mu
- merge
- split_h5mu_train_test
- split_h5mu
- split_modalities
- demux
- bcl2fastq
- bcl_convert
- cellranger_atac_mkfastq
- cellranger_mkfastq
- dimred
- densmap
- lsi
- pca
- tsne
- umap
- download
- download_file
- sync_test_resources
- feature_annotation
- align_query_reference
- 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_scrublet
- intersect_obs
- remove_modality
- subset_h5mu
- subset_obsp
- 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_atac_count
- 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
- 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_atac_qc_metrics
- calculate_qc_metrics
- fastqc
- multiqc
- query/cellxgene_census
- reference
- build_bdrhap_reference
- build_cellranger_arc_reference
- build_cellranger_reference
- build_star_reference
- cellranger_mkgtf
- make_reference
- report/mermaid
- scgpt
- binning
- cell_type_annotation
- cross_check_genes
- embedding
- pad_tokenize
- transfer/publish
- transform
- bpcells_regress_out
- clr
- delete_layer
- log1p
- move_layer
- normalize_total
- regress_out
- scale
- tfidf
- velocity
- scvelo
- velocyto
- nextflow
- annotate
- celltypist
- onclass
- popv
- random_forest_annotation
- scanvi
- svm_annotation
- 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_h5ad_to_seurat
- from_h5mu_to_h5ad
- from_h5mu_to_seurat
- velocyto_to_h5mu
- correction
- cellbender_remove_background_v0_2
- cellbender_remove_background
- dataflow
- concatenate_h5mu
- merge
- split_h5mu_train_test
- split_h5mu
- split_modalities
- demux
- bcl2fastq
- bcl_convert
- cellranger_atac_mkfastq
- cellranger_mkfastq
- dimred
- densmap
- lsi
- pca
- tsne
- umap
- download
- download_file
- sync_test_resources
- feature_annotation
- align_query_reference
- highly_variable_features_scanpy
- score_genes_cell_cycle_scanpy
- files/make_params
- filter
- delimit_fraction
- do_filter
- filter_with_counts
- filter_with_scrublet
- intersect_obs
- remove_modality
- subset_h5mu
- subset_obsp
- 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_atac_count
- 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
- 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_atac_qc_metrics
- calculate_qc_metrics
- fastqc
- multiqc
- query/cellxgene_census
- reference
- build_bdrhap_reference
- build_cellranger_arc_reference
- build_cellranger_reference
- build_star_reference
- cellranger_mkgtf
- make_reference
- report/mermaid
- scgpt
- binning
- cell_type_annotation
- cross_check_genes
- embedding
- pad_tokenize
- transfer/publish
- transform
- bpcells_regress_out
- clr
- delete_layer
- log1p
- move_layer
- normalize_total
- regress_out
- scale
- tfidf
- velocity
- scvelo
- velocyto
- workflows
- annotation
- harmony_knn
- scanvi_scarches
- scgpt_annotation
- scvi_knn
- gdo/gdo_singlesample
- ingestion
- bd_rhapsody
- cellranger_mapping
- cellranger_multi
- cellranger_postprocessing
- conversion
- demux
- make_reference
- integration
- bbknn_leiden
- harmony_leiden
- scanorama_leiden
- scgpt_leiden
- scvi_leiden
- totalvi_leiden
- multiomics
- dimensionality_reduction
- neighbors_leiden_umap
- process_batches
- process_samples
- split_h5mu
- split_modalities
- prot
- prot_multisample
- prot_singlesample
- qc/qc
- rna
- rna_multisample
- rna_singlesample
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