Scarf
0.8.5
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Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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P
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R
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S
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T
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U
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Z
A
active_index() (scarf.metadata.MetaData method)
add_percent_feature() (scarf.assay.Assay method)
ADTassay (class in scarf.assay)
Assay (class in scarf.assay)
assayFeats (scarf.readers.CrH5Reader attribute)
(scarf.readers.CrReader attribute)
assayGroup (scarf.writers.ZarrMerge attribute)
assayName (scarf.writers.H5adToZarr attribute)
(scarf.writers.LoomToZarr attribute)
(scarf.writers.NaboH5ToZarr attribute)
(scarf.writers.SparseToZarr attribute)
assayNames (scarf.datastore.BaseDataStore attribute)
(scarf.datastore.GraphDataStore attribute)
(scarf.datastore.MappingDatastore attribute)
assays (scarf.writers.ZarrMerge attribute)
ATACassay (class in scarf.assay)
attrs (scarf.assay.Assay attribute)
auto_filter_cells() (scarf.DataStore method)
autoNames (scarf.readers.CrH5Reader attribute)
(scarf.readers.CrReader attribute)
B
BaseDataStore (class in scarf.datastore)
C
catNamesKey (scarf.readers.H5adReader attribute)
cell_ids() (scarf.readers.H5adReader method)
(scarf.readers.LoomReader method)
(scarf.readers.NaboH5Reader method)
cell_names() (scarf.readers.CrReader method)
(scarf.readers.LoomReader method)
cellAttrsKey (scarf.readers.H5adReader attribute)
(scarf.readers.LoomReader attribute)
cellIdsKey (scarf.readers.H5adReader attribute)
cellNamesKey (scarf.readers.LoomReader attribute)
cells (scarf.assay.Assay attribute)
(scarf.datastore.BaseDataStore attribute)
(scarf.datastore.GraphDataStore attribute)
(scarf.datastore.MappingDatastore attribute)
chunkSizes (scarf.writers.CrToZarr attribute)
(scarf.writers.H5adToZarr attribute)
(scarf.writers.LoomToZarr attribute)
(scarf.writers.MtxToZarr attribute)
(scarf.writers.NaboH5ToZarr attribute)
(scarf.writers.SparseToZarr attribute)
close() (scarf.readers.CrH5Reader method)
columns (scarf.metadata.MetaData property)
consume() (scarf.readers.CrDirReader method)
(scarf.readers.CrH5Reader method)
(scarf.readers.CrReader method)
(scarf.readers.H5adReader method)
(scarf.readers.LoomReader method)
(scarf.readers.MtxDirReader method)
(scarf.readers.NaboH5Reader method)
consume_dataset() (scarf.readers.H5adReader method)
consume_group() (scarf.readers.H5adReader method)
cr (scarf.writers.CrToZarr attribute)
(scarf.writers.MtxToZarr attribute)
CrDirReader (class in scarf.readers)
create_zarr_count_assay() (in module scarf.writers)
create_zarr_dataset() (in module scarf.writers)
create_zarr_obj_array() (in module scarf.writers)
CrH5Reader (class in scarf.readers)
CrReader (class in scarf.readers)
CrToZarr (class in scarf.writers)
csr_mat (scarf.writers.SparseToZarr attribute)
D
dask_to_zarr() (in module scarf.writers)
DataStore (class in scarf)
drop() (scarf.metadata.MetaData method)
dump() (scarf.writers.CrToZarr method)
(scarf.writers.H5adToZarr method)
(scarf.writers.LoomToZarr method)
(scarf.writers.MtxToZarr method)
(scarf.writers.NaboH5ToZarr method)
(scarf.writers.SparseToZarr method)
E
export_markers_to_csv() (scarf.DataStore method)
F
feat_ids() (scarf.readers.H5adReader method)
(scarf.readers.NaboH5Reader method)
feat_names() (scarf.readers.H5adReader method)
(scarf.readers.NaboH5Reader method)
featCollection (scarf.writers.ZarrMerge attribute)
featIdsKey (scarf.readers.H5adReader attribute)
featNamesKey (scarf.readers.H5adReader attribute)
featOrder (scarf.writers.ZarrMerge attribute)
feats (scarf.assay.Assay attribute)
feature_ids() (scarf.readers.CrReader method)
(scarf.readers.LoomReader method)
feature_names() (scarf.readers.CrReader method)
(scarf.readers.LoomReader method)
feature_types() (scarf.readers.CrReader method)
featureAttrsKey (scarf.readers.H5adReader attribute)
(scarf.readers.LoomReader attribute)
featureIdsKey (scarf.readers.LoomReader attribute)
featureNamesKey (scarf.readers.LoomReader attribute)
fetch() (scarf.metadata.MetaData method)
fetch_all() (scarf.metadata.MetaData method)
filter_cells() (scarf.DataStore method)
fn (scarf.writers.CrToZarr attribute)
(scarf.writers.H5adToZarr attribute)
(scarf.writers.LoomToZarr attribute)
(scarf.writers.MtxToZarr attribute)
(scarf.writers.NaboH5ToZarr attribute)
(scarf.writers.SparseToZarr attribute)
G
get_cell_attrs() (scarf.readers.LoomReader method)
get_cell_columns() (scarf.readers.H5adReader method)
get_cell_vals() (scarf.datastore.BaseDataStore method)
get_dtype() (scarf.metadata.MetaData method)
get_feat_columns() (scarf.readers.H5adReader method)
get_feature_attrs() (scarf.readers.LoomReader method)
get_imputed() (scarf.datastore.GraphDataStore method)
get_index_by() (scarf.metadata.MetaData method)
get_mapping_score() (scarf.datastore.MappingDatastore method)
get_markers() (scarf.DataStore method)
get_target_classes() (scarf.datastore.MappingDatastore method)
GraphDataStore (class in scarf.datastore)
grep() (scarf.metadata.MetaData method)
groupCodes (scarf.readers.H5adReader attribute)
grp (scarf.readers.CrH5Reader attribute)
grpNames (scarf.readers.CrH5Reader attribute)
(scarf.readers.CrReader attribute)
H
h5 (scarf.readers.H5adReader attribute)
(scarf.readers.LoomReader attribute)
(scarf.readers.NaboH5Reader attribute)
(scarf.writers.NaboH5ToZarr attribute)
h5ad (scarf.writers.H5adToZarr attribute)
H5adReader (class in scarf.readers)
H5adToZarr (class in scarf.writers)
h5obj (scarf.readers.CrH5Reader attribute)
head() (scarf.metadata.MetaData method)
I
index (scarf.metadata.MetaData attribute)
index_to_bool() (scarf.metadata.MetaData method)
insert() (scarf.metadata.MetaData method)
L
load_graph() (scarf.datastore.GraphDataStore method)
load_unified_graph() (scarf.datastore.MappingDatastore method)
loc (scarf.readers.CrDirReader attribute)
(scarf.readers.MtxDirReader attribute)
locations (scarf.metadata.MetaData attribute)
loom (scarf.writers.LoomToZarr attribute)
LoomReader (class in scarf.readers)
LoomToZarr (class in scarf.writers)
M
make_bulk() (scarf.DataStore method)
make_graph() (scarf.datastore.GraphDataStore method)
MappingDatastore (class in scarf.datastore)
mark_hvgs() (scarf.assay.RNAassay method)
(scarf.DataStore method)
mark_prevalent_peaks() (scarf.assay.ATACassay method)
(scarf.DataStore method)
matFn (scarf.readers.CrDirReader attribute)
(scarf.readers.MtxDirReader attribute)
matrix_key (scarf.readers.H5adReader attribute)
matrixDtype (scarf.readers.H5adReader attribute)
(scarf.readers.LoomReader attribute)
matrixKey (scarf.readers.LoomReader attribute)
mergedCells (scarf.writers.ZarrMerge attribute)
mergedFeats (scarf.writers.ZarrMerge attribute)
MetaData (class in scarf.metadata)
module
scarf.metadata
scarf.readers
scarf.writers
mount_location() (scarf.metadata.MetaData method)
MtxDirReader (class in scarf.readers)
MtxToZarr (class in scarf.writers)
multi_sift() (scarf.metadata.MetaData method)
N
N (scarf.metadata.MetaData attribute)
NaboH5Reader (class in scarf.readers)
NaboH5ToZarr (class in scarf.writers)
name (scarf.assay.Assay attribute)
names (scarf.writers.ZarrMerge attribute)
nCells (scarf.readers.CrH5Reader attribute)
(scarf.readers.CrReader attribute)
(scarf.readers.H5adReader attribute)
(scarf.readers.LoomReader attribute)
(scarf.readers.NaboH5Reader attribute)
(scarf.writers.ZarrMerge attribute)
nFeats (scarf.writers.ZarrMerge attribute)
nFeatures (scarf.readers.CrH5Reader attribute)
(scarf.readers.CrReader attribute)
(scarf.readers.H5adReader attribute)
(scarf.readers.LoomReader attribute)
(scarf.readers.NaboH5Reader attribute)
normed() (scarf.assay.ADTassay method)
(scarf.assay.Assay method)
(scarf.assay.ATACassay method)
(scarf.assay.RNAassay method)
normMethod (scarf.assay.Assay attribute)
nthreads (scarf.assay.Assay attribute)
(scarf.datastore.BaseDataStore attribute)
(scarf.datastore.GraphDataStore attribute)
(scarf.datastore.MappingDatastore attribute)
P
plot_cells_dists() (scarf.DataStore method)
plot_cluster_tree() (scarf.DataStore method)
plot_layout() (scarf.DataStore method)
plot_marker_heatmap() (scarf.DataStore method)
plot_unified_layout() (scarf.datastore.MappingDatastore method)
R
rawData (scarf.assay.Assay attribute)
remove_trend() (scarf.metadata.MetaData method)
rename_assays() (scarf.readers.CrReader method)
reset_key() (scarf.metadata.MetaData method)
RNAassay (class in scarf.assay)
run_cell_cycle_scoring() (scarf.DataStore method)
run_clustering() (scarf.datastore.GraphDataStore method)
run_leiden_clustering() (scarf.datastore.GraphDataStore method)
run_mapping() (scarf.datastore.MappingDatastore method)
run_marker_search() (scarf.DataStore method)
run_pseudotime_scoring() (scarf.datastore.GraphDataStore method)
run_topacedo_sampler() (scarf.datastore.GraphDataStore method)
run_tsne() (scarf.datastore.GraphDataStore method)
run_umap() (scarf.datastore.GraphDataStore method)
run_unified_tsne() (scarf.datastore.MappingDatastore method)
run_unified_umap() (scarf.datastore.MappingDatastore method)
S
save_normalized_data() (scarf.assay.Assay method)
scarf.metadata
module
scarf.readers
module
scarf.writers
module
score_features() (scarf.assay.Assay method)
set_default_assay() (scarf.datastore.BaseDataStore method)
set_feature_stats() (scarf.assay.ATACassay method)
(scarf.assay.RNAassay method)
sf (scarf.assay.Assay attribute)
show_zarr_tree() (scarf.DataStore method)
sift() (scarf.metadata.MetaData method)
SparseToZarr (class in scarf.writers)
subset_assay_zarr() (in module scarf.writers)
T
to_anndata() (scarf.DataStore method)
to_pandas_dataframe() (scarf.metadata.MetaData method)
to_raw_sparse() (scarf.assay.Assay method)
to_sparse() (scarf.readers.CrDirReader method)
(scarf.readers.MtxDirReader method)
U
unmount_location() (scarf.metadata.MetaData method)
update_key() (scarf.metadata.MetaData method)
Z
z (scarf.assay.Assay attribute)
(scarf.datastore.BaseDataStore attribute)
(scarf.datastore.GraphDataStore attribute)
(scarf.datastore.MappingDatastore attribute)
(scarf.writers.CrToZarr attribute)
(scarf.writers.H5adToZarr attribute)
(scarf.writers.LoomToZarr attribute)
(scarf.writers.MtxToZarr attribute)
(scarf.writers.NaboH5ToZarr attribute)
(scarf.writers.SparseToZarr attribute)
(scarf.writers.ZarrMerge attribute)
ZarrMerge (class in scarf.writers)
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v: 0.8.5
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