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morris-lab
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CellOracle
This is the alpha version of the CellOracle package
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Scan motifs error! tfi.scan(fpr=0.02,motifs=motifs, verbose=True)
#216
zjprookie
opened
23 hours ago
1
Bulk-ATAC-seq data - distal cis-regulatory elements annotation
#215
gosiagolda
closed
3 weeks ago
0
ImportError: cannot import name 'default_motifs' from 'gimmemotifs.motif'
#214
chuyaowang
opened
4 weeks ago
0
(Best practices) Is adding TF-target gene pairs manually required if I have generated the base_GRN from snATAC seq?
#213
yojetsharma
opened
4 weeks ago
0
I am getting chekered plots upon running the links.plot function, how to correct this?
#212
yojetsharma
closed
1 month ago
1
'ColormapRegistry' object has no attribute 'get_cmap'
#211
imraanGit
opened
1 month ago
0
How to proceed if we don't have enough information to manually make a TF-target gene pair data?
#210
yojetsharma
opened
1 month ago
0
Producing a video visualisation (like shown on https://celloracle.org/)
#209
jdarmitage
opened
1 month ago
0
seuratToAnndata
#208
nhu-github
opened
2 months ago
0
The Kernel crashed when I run tfi.scan
#207
Zhangruiqi111
opened
2 months ago
0
Error in calculating embedding shift
#206
Larrycpan
closed
2 months ago
3
does not have enough regulatory connection in the GRNs. Cannot perform simulation.
#205
xiaomaolxc
opened
2 months ago
0
Does celloracle need pseudotime information to give cluster wise GRNs?
#204
ruchikabhat
opened
2 months ago
0
Saving plots as individual files?
#203
njrobins
closed
3 months ago
2
GimmeMotifs installed but can't install celloracle because of 'Failed building wheel for gimmemotifs'
#202
jianwu1
opened
4 months ago
1
Can't convert from Seurat to anndata #8928
#201
xiaomaolxc
closed
2 months ago
0
We don't have default motifs for your species, Please specify motif data by yourself.
#200
Roger-GOAT
opened
4 months ago
1
Loading CellOracle takes too much time
#199
CYWu111
opened
4 months ago
0
Loading CellOracle takes too much time.
#198
xmuhuanglab
closed
4 months ago
0
Heterogeneous dataset subsetting and number of cells/cluster
#197
acv21
opened
4 months ago
0
Fixed inconsistent results of `oracle.get_links` across runs
#196
PauBadiaM
opened
4 months ago
0
model overfitting
#195
tkisss
opened
5 months ago
0
Request for 3D UMAP
#194
fafa92
opened
5 months ago
0
Problem when using a custom genomes_dir for TF scan
#193
VictorCurean
opened
5 months ago
2
Plot cell types under 'development' flow grid
#192
alexandrelanau
opened
6 months ago
0
tfinfo and GRN files
#191
momur
opened
6 months ago
4
WinError: FileNotFound at installation
#190
VictorCurean
closed
6 months ago
1
Request for Schistosoma japonicum genome
#189
shycheng
opened
6 months ago
0
editing the evaluate_and_plot_simulation_value_distribution function
#188
Alireza-Majd
closed
6 months ago
1
tfi.scan error:
#187
Edsan17
closed
6 months ago
3
Building Base GRN with multiple samples
#186
shahrozeabbas
opened
6 months ago
0
Vector Plots
#185
sarah-chapin
opened
6 months ago
1
Projecting the simulated flows on a specific cluster
#184
jyang635
opened
7 months ago
1
Error with data_conversion.seurat_object_to_anndata
#183
JunyanKan
closed
6 months ago
1
Adding new reference genome: Rn7
#182
MartijnLvandenBroek
opened
7 months ago
0
Installation issue on Mac book pro/ VS Code
#181
jw235
opened
7 months ago
4
New genomes promoter_based_GRN
#180
dnjst
opened
8 months ago
0
Problems with ma.get_tss_info function
#179
niklasbinder
closed
8 months ago
3
TypeError: BaggingRegressor 'base_estimator'
#178
iichelhadi
closed
8 months ago
4
Can we make custom genome annotation by custom gff and fasta file?
#177
duchen-whu
opened
8 months ago
0
Question about edge filtering strategy of CellOracle
#176
R-Krait
opened
8 months ago
0
Estimating cell density after perturbation
#175
jordiabante
opened
8 months ago
0
The kernel keep dying during TF motif scan.
#174
Lukas20170
closed
8 months ago
0
How to check the available TF list in the oracle object
#173
YuchenXiangEMBL
closed
6 months ago
1
Error with oracle.import_anndata_as_raw_count
#172
Hanxi-002
closed
6 months ago
1
Failed to load celloracle
#171
YuchenXiangEMBL
opened
8 months ago
2
AttributeError following co.data_conversion.seurat_object_to_anndata(
#170
A-legac45
closed
8 months ago
1
More than 3000 genes
#169
sarah-chapin
opened
9 months ago
1
Is CellOracle suitable for analysing cross-organ development for the same cell type?@JiaGuangshuai
#168
Counts-Xin
opened
9 months ago
0
gene selection from loaded seurat object
#167
A-legac45
closed
9 months ago
3
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