File tree
510 files changed
+1020
-1018
lines changed- .github/workflows
- 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_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
- 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
- duplicate_obs
- duplicate_var
- 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_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_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
- 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
- duplicate_obs
- duplicate_var
- 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_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
- 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
- process_batches
- process_samples
- split_modalities
- prot
- prot_multisample
- prot_singlesample
- qc/qc
- rna
- rna_multisample
- rna_singlesample
Some content is hidden
Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.
510 files changed
+1020
-1018
lines changed| Original file line number | Diff line number | Diff line change | |
|---|---|---|---|
| |||
193 | 193 | | |
194 | 194 | | |
195 | 195 | | |
196 | | - | |
| 196 | + | |
| 197 | + | |
| 198 | + | |
| Original file line number | Diff line number | Diff line change | |
|---|---|---|---|
| |||
1 | | - | |
| 1 | + | |
2 | 2 | | |
3 | 3 | | |
4 | 4 | | |
| |||
| Original file line number | Diff line number | Diff line change | |
|---|---|---|---|
| |||
394 | 394 | | |
395 | 395 | | |
396 | 396 | | |
397 | | - | |
| 397 | + | |
398 | 398 | | |
399 | | - | |
| 399 | + | |
400 | 400 | | |
401 | 401 | | |
402 | 402 | | |
| |||
| Original file line number | Diff line number | Diff line change | |
|---|---|---|---|
| |||
596 | 596 | | |
597 | 597 | | |
598 | 598 | | |
599 | | - | |
| 599 | + | |
600 | 600 | | |
601 | | - | |
| 601 | + | |
602 | 602 | | |
603 | 603 | | |
604 | 604 | | |
| |||
| Original file line number | Diff line number | Diff line change | |
|---|---|---|---|
| |||
336 | 336 | | |
337 | 337 | | |
338 | 338 | | |
339 | | - | |
| 339 | + | |
340 | 340 | | |
341 | | - | |
| 341 | + | |
342 | 342 | | |
343 | 343 | | |
344 | 344 | | |
| |||
| Original file line number | Diff line number | Diff line change | |
|---|---|---|---|
| |||
561 | 561 | | |
562 | 562 | | |
563 | 563 | | |
564 | | - | |
| 564 | + | |
565 | 565 | | |
566 | | - | |
| 566 | + | |
567 | 567 | | |
568 | 568 | | |
569 | 569 | | |
| |||
| Original file line number | Diff line number | Diff line change | |
|---|---|---|---|
| |||
351 | 351 | | |
352 | 352 | | |
353 | 353 | | |
354 | | - | |
| 354 | + | |
355 | 355 | | |
356 | | - | |
| 356 | + | |
357 | 357 | | |
358 | 358 | | |
359 | 359 | | |
| |||
| Original file line number | Diff line number | Diff line change | |
|---|---|---|---|
| |||
561 | 561 | | |
562 | 562 | | |
563 | 563 | | |
564 | | - | |
| 564 | + | |
565 | 565 | | |
566 | | - | |
| 566 | + | |
567 | 567 | | |
568 | 568 | | |
569 | 569 | | |
| |||
Lines changed: 2 additions & 2 deletions
| Original file line number | Diff line number | Diff line change | |
|---|---|---|---|
| |||
355 | 355 | | |
356 | 356 | | |
357 | 357 | | |
358 | | - | |
| 358 | + | |
359 | 359 | | |
360 | | - | |
| 360 | + | |
361 | 361 | | |
362 | 362 | | |
363 | 363 | | |
| |||
Lines changed: 2 additions & 2 deletions
| Original file line number | Diff line number | Diff line change | |
|---|---|---|---|
| |||
576 | 576 | | |
577 | 577 | | |
578 | 578 | | |
579 | | - | |
| 579 | + | |
580 | 580 | | |
581 | | - | |
| 581 | + | |
582 | 582 | | |
583 | 583 | | |
584 | 584 | | |
| |||
0 commit comments