Index

Symbols

--samtools-memory <samtools_memory> velocyto-run command line option velocyto-run-dropest command line option velocyto-run10x command line option --version velocyto command line option -@, --samtools-threads <samtools_threads> velocyto-run command line option velocyto-run-dropest command line option velocyto-run10x command line option -b, --bcfile <bcfile> velocyto-run command line option velocyto-run-dropest command line option -c, --onefilepercell velocyto-run command line option -d, --dump <dump> velocyto-run command line option velocyto-run-dropest command line option velocyto-run-smartseq2 command line option velocyto-run10x command line option -e, --sampleid <sampleid> velocyto-run command line option velocyto-run-dropest command line option velocyto-run-smartseq2 command line option -l, --logic <logic> velocyto-run command line option velocyto-run-dropest command line option velocyto-run10x command line option -m, --mask <mask> velocyto-run command line option velocyto-run10x command line option

-M, --multimap velocyto-run command line option velocyto-run10x command line option -m, --repmask <repmask> velocyto-run-dropest command line option velocyto-run-smartseq2 command line option -o, --corrected-output <corrected_output> velocyto-tools-dropest-bc-correct command line option -o, --outputfolder <outputfolder> velocyto-run command line option velocyto-run-dropest command line option velocyto-run-smartseq2 command line option -s, --metadatatable <metadatatable> velocyto-run command line option velocyto-run10x command line option -t, --dtype <dtype> velocyto-run command line option velocyto-run-dropest command line option velocyto-run-smartseq2 command line option velocyto-run10x command line option -u, --umi-extension <umi_extension> velocyto-run command line option -U, --without-umi velocyto-run command line option -v, --verbose velocyto-run command line option velocyto-run-dropest command line option velocyto-run-smartseq2 command line option velocyto-run10x command line option

A

accept_discordant (velocyto.logic.Discordant10X attribute) (velocyto.logic.Intermediate10X attribute) (velocyto.logic.Logic attribute) (velocyto.logic.ObservedSpanning10X attribute) (velocyto.logic.Permissive10X attribute) (velocyto.logic.SmartSeq2 attribute) (velocyto.logic.ValidatedIntrons10X attribute)

add_mappings_record() (velocyto.molitem.Molitem method) adjust_totS_totU() (velocyto.analysis.VelocytoLoom method) append_exon() (velocyto.transcript_model.TranscriptModel method) assign_indexes_to_genes() (velocyto.counter.ExInCounter method)

B

balance_knn_loop (in module velocyto.neighbors) balance_knn_loop_constrained (in module velocyto.neighbors) BalancedKNN (class in velocyto.neighbors) BAMFILE velocyto-run command line option velocyto-run-dropest command line option

BAMFILEPATH velocyto-tools-dropest-bc-correct command line option BAMFILES velocyto-run-smartseq2 command line option bc (velocyto.read.Read attribute)

C

calculate_embedding_shift() (velocyto.analysis.VelocytoLoom method) calculate_grid_arrows() (velocyto.analysis.VelocytoLoom method) calculate_shift() (velocyto.analysis.VelocytoLoom method) calculate_velocity() (velocyto.analysis.VelocytoLoom method) chop_if_long_intron() (velocyto.transcript_model.TranscriptModel method) chrom (velocyto.gene_info.GeneInfo attribute) (velocyto.read.Read attribute) chromstrand (velocyto.transcript_model.TranscriptModel attribute) clip3 (velocyto.read.Read attribute) clip5 (velocyto.read.Read attribute) cluster_ix (velocyto.analysis.VelocytoLoom attribute) cluster_uid (velocyto.analysis.VelocytoLoom attribute) clusters_stats() (in module velocyto.estimation) colDeltaCor() (in module velocyto.estimation) colDeltaCorLog10() (in module velocyto.estimation) colDeltaCorLog10partial() (in module velocyto.estimation) colDeltaCorpartial() (in module velocyto.estimation)

colDeltaCorSqrt() (in module velocyto.estimation) colDeltaCorSqrtpartial() (in module velocyto.estimation) colormap_fun() (in module velocyto.analysis) compute_transition_matrix() (velocyto.diffusion.Diffusion method) compute_transition_matrix2() (velocyto.diffusion.Diffusion method) connectivity_to_weights() (in module velocyto.neighbors) contains() (velocyto.feature.Feature method) convolve_by_sparse_weights() (in module velocyto.neighbors) count() (velocyto.counter.ExInCounter method) (velocyto.logic.Discordant10X method) (velocyto.logic.Intermediate10X method) (velocyto.logic.Logic method) (velocyto.logic.ObservedSpanning10X method) (velocyto.logic.Permissive10X method) (velocyto.logic.SmartSeq2 method) (velocyto.logic.Stricter10X method) (velocyto.logic.ValidatedIntrons10X method) custom_filter_attributes() (velocyto.analysis.VelocytoLoom method)

D

Default (in module velocyto.logic) default_filter_and_norm() (velocyto.analysis.VelocytoLoom method) default_fit_preparation() (velocyto.analysis.VelocytoLoom method) dictionary_intersect() (in module velocyto.molitem) dictionary_union() (in module velocyto.molitem) diffuse() (velocyto.diffusion.Diffusion method)

Diffusion (class in velocyto.diffusion) Discordant10X (class in velocyto.logic) doesnt_start_after() (velocyto.feature.Feature method) DROPEST_OUT velocyto-tools-dropest-bc-correct command line option dump_hdf5() (in module velocyto.serialization)

E

end (velocyto.feature.Feature attribute) (velocyto.gene_info.GeneInfo attribute) (velocyto.read.Read attribute) (velocyto.transcript_model.TranscriptModel attribute) end_overlaps_with_part_of() (velocyto.feature.Feature method)

ends_upstream_of() (velocyto.feature.Feature method) (velocyto.transcript_model.TranscriptModel method) estimate_transition_prob() (velocyto.analysis.VelocytoLoom method) exin_no (velocyto.feature.Feature attribute) ExInCounter (class in velocyto.counter) extrapolate_cell_at_t() (velocyto.analysis.VelocytoLoom method)

F

Feature (class in velocyto.feature) feature (velocyto.segment_match.SegmentMatch attribute) FeatureIndex (class in velocyto.indexes) filter_cells() (velocyto.analysis.VelocytoLoom method) filter_genes() (velocyto.analysis.VelocytoLoom method) filter_genes_by_phase_portrait() (velocyto.analysis.VelocytoLoom method) filter_genes_good_fit() (velocyto.analysis.VelocytoLoom method)

find_overlapping_ivls() (velocyto.indexes.FeatureIndex method) find_overlapping_trascript_models() (velocyto.indexes.TransciptsIndex method) fit() (velocyto.neighbors.BalancedKNN method) fit_gammas() (velocyto.analysis.VelocytoLoom method) fit_slope() (in module velocyto.estimation) fit_slope_offset() (in module velocyto.estimation) fit_slope_weighted() (in module velocyto.estimation) fit_slope_weighted_offset() (in module velocyto.estimation)

G

gaussian_kernel() (in module velocyto.analysis) gene_knn_imputation() (velocyto.analysis.VelocytoLoom method) geneid (velocyto.gene_info.GeneInfo attribute) (velocyto.transcript_model.TranscriptModel attribute) GeneInfo (class in velocyto.gene_info) genename (velocyto.gene_info.GeneInfo attribute) (velocyto.transcript_model.TranscriptModel attribute)

get_downstream_exon() (velocyto.feature.Feature method) get_upstream_exon() (velocyto.feature.Feature method) GTFFILE velocyto-run command line option velocyto-run-dropest command line option velocyto-run-smartseq2 command line option velocyto-run10x command line option

H

has_ivls_enclosing() (velocyto.indexes.FeatureIndex method)

I

Intermediate10X (class in velocyto.logic) intersects() (velocyto.feature.Feature method) (velocyto.transcript_model.TranscriptModel method) is_last_3prime (velocyto.feature.Feature attribute)

is_spliced (velocyto.read.Read attribute) (velocyto.segment_match.SegmentMatch attribute) is_validated (velocyto.feature.Feature attribute) iter_alignments() (velocyto.counter.ExInCounter method) ixs_thatsort_a2b() (in module velocyto.analysis)

K

kind (velocyto.feature.Feature attribute) kneighbors() (velocyto.neighbors.BalancedKNN method) kneighbors_graph() (velocyto.neighbors.BalancedKNN method) knn_balance() (in module velocyto.neighbors)

knn_distance_matrix() (in module velocyto.neighbors) knn_imputation() (velocyto.analysis.VelocytoLoom method) knn_imputation_precomputed() (velocyto.analysis.VelocytoLoom method) knn_smooth_weights() (in module velocyto.neighbors)

L

last_interval_not_reached (velocyto.indexes.FeatureIndex attribute) layers (velocyto.logic.Discordant10X attribute) (velocyto.logic.Intermediate10X attribute) (velocyto.logic.Logic attribute) (velocyto.logic.ObservedSpanning10X attribute) (velocyto.logic.Permissive10X attribute) (velocyto.logic.SmartSeq2 attribute) (velocyto.logic.Stricter10X attribute) (velocyto.logic.ValidatedIntrons10X attribute)

list_features (velocyto.transcript_model.TranscriptModel attribute) load_hdf5() (in module velocyto.serialization) load_velocyto_hdf5() (in module velocyto.analysis) Logic (class in velocyto.logic)

M

make_mutual() (in module velocyto.neighbors) mappings_record (velocyto.molitem.Molitem attribute) maps_to_exon (velocyto.segment_match.SegmentMatch attribute) maps_to_intron (velocyto.segment_match.SegmentMatch attribute)

mark_overlapping_ivls() (velocyto.indexes.FeatureIndex method) mark_up_introns() (velocyto.counter.ExInCounter method) maxtidx (velocyto.indexes.TransciptsIndex attribute) min_n() (in module velocyto.neighbors) Molitem (class in velocyto.molitem)

N

n_samples (velocyto.neighbors.BalancedKNN attribute) normalize() (velocyto.analysis.VelocytoLoom method) normalize_by_size_factor() (velocyto.analysis.VelocytoLoom method)

normalize_by_total() (velocyto.analysis.VelocytoLoom method) normalize_median() (velocyto.analysis.VelocytoLoom method) numba_random_seed (in module velocyto.analysis)

O

ObservedSpanning10X (class in velocyto.logic)

P

parse_cigar_tuple() (velocyto.counter.ExInCounter static method) pcount() (velocyto.counter.ExInCounter method) pcount_cell_batch() (velocyto.counter.ExInCounter method) peek() (velocyto.counter.ExInCounter method) peek_and_correct() (velocyto.counter.ExInCounter method) peek_umi_only() (velocyto.counter.ExInCounter method) perform_PCA() (velocyto.analysis.VelocytoLoom method) perform_TSNE() (velocyto.analysis.VelocytoLoom method) perform_validation_markup (velocyto.logic.Discordant10X attribute) (velocyto.logic.Intermediate10X attribute) (velocyto.logic.Logic attribute) (velocyto.logic.ObservedSpanning10X attribute) (velocyto.logic.Permissive10X attribute) (velocyto.logic.SmartSeq2 attribute) (velocyto.logic.Stricter10X attribute) (velocyto.logic.ValidatedIntrons10X attribute)

Permissive10X (class in velocyto.logic) permute_rows_nsign (in module velocyto.analysis) plot_arrows_embedding() (velocyto.analysis.VelocytoLoom method) plot_cell_transitions() (velocyto.analysis.VelocytoLoom method) plot_expression_as_color() (velocyto.analysis.VelocytoLoom method) plot_fractions() (velocyto.analysis.VelocytoLoom method) plot_grid_arrows() (velocyto.analysis.VelocytoLoom method) plot_pca() (velocyto.analysis.VelocytoLoom method) plot_phase_portraits() (velocyto.analysis.VelocytoLoom method) plot_velocity_as_color() (velocyto.analysis.VelocytoLoom method) pos (velocyto.read.Read attribute) predict_U() (velocyto.analysis.VelocytoLoom method) prepare_markov() (velocyto.analysis.VelocytoLoom method)

R

Read (class in velocyto.read) read_repeats() (velocyto.counter.ExInCounter method) read_transcriptmodels() (velocyto.counter.ExInCounter method) ref_skipped (velocyto.read.Read attribute)

reload_raw() (velocyto.analysis.VelocytoLoom method) reset() (velocyto.indexes.FeatureIndex method) reverse() (in module velocyto.counter) robust_size_factor() (velocyto.analysis.VelocytoLoom method) run_markov() (velocyto.analysis.VelocytoLoom method)

S

SAMPLEFOLDER velocyto-run10x command line option scale_to_match_median() (in module velocyto.analysis) scan_not_terminated (velocyto.indexes.TransciptsIndex attribute) scatter_viz() (in module velocyto.analysis) score_cluster_expression() (velocyto.analysis.VelocytoLoom method) score_cv_vs_mean() (velocyto.analysis.VelocytoLoom method) score_detection_levels() (velocyto.analysis.VelocytoLoom method) segment (velocyto.segment_match.SegmentMatch attribute) SegmentMatch (class in velocyto.segment_match) segments (velocyto.read.Read attribute) set_clusters() (velocyto.analysis.VelocytoLoom method) skip_makes_sense (velocyto.segment_match.SegmentMatch attribute) SmartSeq2 (class in velocyto.logic) smooth_data() (velocyto.neighbors.BalancedKNN method) span (velocyto.read.Read attribute)

start (velocyto.feature.Feature attribute) (velocyto.gene_info.GeneInfo attribute) (velocyto.read.Read attribute) (velocyto.transcript_model.TranscriptModel attribute) start_overlaps_with_part_of() (velocyto.feature.Feature method) strand (velocyto.gene_info.GeneInfo attribute) (velocyto.read.Read attribute) stranded (velocyto.logic.Discordant10X attribute) (velocyto.logic.Intermediate10X attribute) (velocyto.logic.Logic attribute) (velocyto.logic.ObservedSpanning10X attribute) (velocyto.logic.Permissive10X attribute) (velocyto.logic.SmartSeq2 attribute) (velocyto.logic.Stricter10X attribute) (velocyto.logic.ValidatedIntrons10X attribute) Stricter10X (class in velocyto.logic)

T

take_top() (in module velocyto.neighbors) tidx (velocyto.indexes.TransciptsIndex attribute) to_hdf5() (velocyto.analysis.VelocytoLoom method) transcipt_models (velocyto.indexes.TransciptsIndex attribute)

TransciptsIndex (class in velocyto.indexes) transcript_model (velocyto.feature.Feature attribute) TranscriptModel (class in velocyto.transcript_model) trid (velocyto.transcript_model.TranscriptModel attribute) trname (velocyto.transcript_model.TranscriptModel attribute)

U

umi (velocyto.read.Read attribute)

V

ValidatedIntrons10X (class in velocyto.logic) velocyto command line option --version velocyto-run command line option --samtools-memory <samtools_memory> -@, --samtools-threads <samtools_threads> -M, --multimap -U, --without-umi -b, --bcfile <bcfile> -c, --onefilepercell -d, --dump <dump> -e, --sampleid <sampleid> -l, --logic <logic> -m, --mask <mask> -o, --outputfolder <outputfolder> -s, --metadatatable <metadatatable> -t, --dtype <dtype> -u, --umi-extension <umi_extension> -v, --verbose BAMFILE GTFFILE velocyto-run-dropest command line option --samtools-memory <samtools_memory> -@, --samtools-threads <samtools_threads> -b, --bcfile <bcfile> -d, --dump <dump> -e, --sampleid <sampleid> -l, --logic <logic> -m, --repmask <repmask> -o, --outputfolder <outputfolder> -t, --dtype <dtype> -v, --verbose BAMFILE GTFFILE velocyto-run-smartseq2 command line option -d, --dump <dump> -e, --sampleid <sampleid> -m, --repmask <repmask> -o, --outputfolder <outputfolder> -t, --dtype <dtype> -v, --verbose BAMFILES GTFFILE

velocyto-run10x command line option --samtools-memory <samtools_memory> -@, --samtools-threads <samtools_threads> -M, --multimap -d, --dump <dump> -l, --logic <logic> -m, --mask <mask> -s, --metadatatable <metadatatable> -t, --dtype <dtype> -v, --verbose GTFFILE SAMPLEFOLDER velocyto-tools-dropest-bc-correct command line option -o, --corrected-output <corrected_output> BAMFILEPATH DROPEST_OUT velocyto.analysis (module) velocyto.counter (module) velocyto.diffusion (module) velocyto.estimation (module) velocyto.feature (module) velocyto.gene_info (module) velocyto.indexes (module) velocyto.logic (module) velocyto.molitem (module) velocyto.neighbors (module) velocyto.read (module) velocyto.segment_match (module) velocyto.serialization (module) velocyto.transcript_model (module) VelocytoLoom (class in velocyto.analysis)