pycistarget
latest
Installation
Methods
SCENIC+ motif collection
Tutorials
API
pycistarget
Index
Edit on GitHub
Index
A
|
B
|
C
|
D
|
F
|
G
|
H
|
I
|
K
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
A
add_motif_annotation_dem() (pycistarget.motif_enrichment_dem.DEM method)
add_motif_annotation_homer() (pycistarget.motif_enrichment_homer.Homer method)
adjpval_thr (pycistarget.motif_enrichment_dem.DEM attribute)
annotation_version (pycistarget.motif_enrichment_homer.Homer attribute)
B
bed_path (pycistarget.motif_enrichment_homer.Homer attribute)
C
cistrome_annotation (pycistarget.motif_enrichment_homer.Homer attribute)
cistromes (pycistarget.motif_enrichment_dem.DEM attribute)
cluster_buster() (in module pycistarget.cluster_buster)
cluster_buster_path (pycistarget.motif_enrichment_dem.DEM attribute)
contrasts (pycistarget.motif_enrichment_dem.DEM attribute)
coord_to_region_names() (in module pycistarget.utils)
create_groups() (in module pycistarget.motif_enrichment_dem)
D
db_scores (pycistarget.motif_enrichment_dem.DEMDatabase attribute)
DEM (class in pycistarget.motif_enrichment_dem)
DEM_internal() (in module pycistarget.motif_enrichment_dem)
DEM_results() (pycistarget.motif_enrichment_dem.DEM method)
DEMDatabase (class in pycistarget.motif_enrichment_dem)
denovo (pycistarget.motif_enrichment_homer.Homer attribute)
denovo_motif_hits (pycistarget.motif_enrichment_homer.Homer attribute)
,
[1]
denovo_motifs (pycistarget.motif_enrichment_homer.Homer attribute)
F
find_motif_hits() (pycistarget.motif_enrichment_homer.Homer method)
fraction_overlap (pycistarget.motif_enrichment_dem.DEM attribute)
G
genome (pycistarget.motif_enrichment_homer.Homer attribute)
genome_annotation (pycistarget.motif_enrichment_dem.DEM attribute)
get_cistrome_per_TF() (in module pycistarget.utils)
get_cistromes() (pycistarget.motif_enrichment_homer.Homer method)
get_cistromes_per_region_set() (in module pycistarget.utils)
get_motif_hits() (in module pycistarget.motif_enrichment_dem)
get_motifs_per_TF() (in module pycistarget.utils)
get_position_index() (in module pycistarget.utils)
get_sequence_names_from_fasta() (in module pycistarget.cluster_buster)
get_TF_list() (in module pycistarget.utils)
grep() (in module pycistarget.cluster_buster)
H
Homer (class in pycistarget.motif_enrichment_homer)
homer2meme() (in module pycistarget.utils)
homer_path (pycistarget.motif_enrichment_homer.Homer attribute)
homer_results() (in module pycistarget.motif_enrichment_homer)
I
inplace_change() (in module pycistarget.utils)
K
known_cistromes (pycistarget.motif_enrichment_homer.Homer attribute)
known_motif_hits (pycistarget.motif_enrichment_homer.Homer attribute)
known_motifs (pycistarget.motif_enrichment_homer.Homer attribute)
L
length (pycistarget.motif_enrichment_homer.Homer attribute)
load_db() (pycistarget.motif_enrichment_dem.DEMDatabase method)
load_denovo() (pycistarget.motif_enrichment_homer.Homer method)
load_known() (pycistarget.motif_enrichment_homer.Homer method)
load_motif_annotations() (in module pycistarget.utils)
log2fc_thr (pycistarget.motif_enrichment_dem.DEM attribute)
M
mask (pycistarget.motif_enrichment_homer.Homer attribute)
max_bg_regions (pycistarget.motif_enrichment_dem.DEM attribute)
mean_fg_thr (pycistarget.motif_enrichment_dem.DEM attribute)
meme_collection_path (pycistarget.motif_enrichment_homer.Homer attribute)
meme_path (pycistarget.motif_enrichment_homer.Homer attribute)
module
pycistarget.cluster_buster
pycistarget.motif_enrichment_dem
pycistarget.motif_enrichment_homer
pycistarget.utils
motif_enrichment (pycistarget.motif_enrichment_dem.DEM attribute)
motif_hit_thr (pycistarget.motif_enrichment_dem.DEM attribute)
motif_hits (pycistarget.motif_enrichment_dem.DEM attribute)
motif_similarity_fdr (pycistarget.motif_enrichment_dem.DEM attribute)
(pycistarget.motif_enrichment_homer.Homer attribute)
motifs_to_use (pycistarget.motif_enrichment_dem.DEM attribute)
N
n_cpu (pycistarget.motif_enrichment_dem.DEM attribute)
name (pycistarget.motif_enrichment_dem.DEM attribute)
(pycistarget.motif_enrichment_homer.Homer attribute)
O
orthologous_identity_threshold (pycistarget.motif_enrichment_dem.DEM attribute)
(pycistarget.motif_enrichment_homer.Homer attribute)
outdir (pycistarget.motif_enrichment_homer.Homer attribute)
P
p_adjust_bh() (in module pycistarget.motif_enrichment_dem)
path_to_genome_fasta (pycistarget.motif_enrichment_dem.DEM attribute)
path_to_motif_annotations (pycistarget.motif_enrichment_dem.DEM attribute)
(pycistarget.motif_enrichment_homer.Homer attribute)
path_to_motifs (pycistarget.motif_enrichment_dem.DEM attribute)
promoter_space (pycistarget.motif_enrichment_dem.DEM attribute)
pycistarget.cluster_buster
module
pycistarget.motif_enrichment_dem
module
pycistarget.motif_enrichment_homer
module
pycistarget.utils
module
pyranges2names() (in module pycistarget.cluster_buster)
R
region_names_to_coordinates() (in module pycistarget.utils)
region_sets (pycistarget.motif_enrichment_dem.DEM attribute)
region_sets_to_signature() (in module pycistarget.utils)
regions_to_db (pycistarget.motif_enrichment_dem.DEM attribute)
(pycistarget.motif_enrichment_dem.DEMDatabase attribute)
run() (pycistarget.motif_enrichment_dem.DEM method)
(pycistarget.motif_enrichment_homer.Homer method)
run_homer() (in module pycistarget.motif_enrichment_homer)
S
shuffle_sequence() (in module pycistarget.motif_enrichment_dem)
size (pycistarget.motif_enrichment_homer.Homer attribute)
specie (pycistarget.motif_enrichment_dem.DEM attribute)
subset_motifs (pycistarget.motif_enrichment_dem.DEM attribute)
T
target_to_query() (in module pycistarget.utils)
tmp_dir (pycistarget.motif_enrichment_dem.DEM attribute)
tomtom() (in module pycistarget.utils)
total_regions (pycistarget.motif_enrichment_dem.DEMDatabase attribute)
Read the Docs
v: latest
Versions
latest
stable
Downloads
On Read the Docs
Project Home
Builds