morris-lab CellOracle issues

morris-lab / CellOracle

This is the alpha version of the CellOracle package

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Strange arrows after gene KO

#221 lh12565 opened 2 weeks ago
0
ma.SUPPORTED_REF_GENOME for new chicken genome: GRCg7b

#220 YuJiandongBio opened 3 weeks ago
0
Retrieving the multi dimensional gene expression shift vector

#219 CBannink opened 1 month ago
0
network_analysis.linkList_to_networkgraph() Creates wrong directed edges

#218 osmanmerdan opened 1 month ago
0
What the the difference between fit_GRN_for_simulation, fit_GRN_for_network_analysis?

#217 swapnilkeshari opened 1 month ago
0
Scan motifs error! tfi.scan(fpr=0.02,motifs=motifs, verbose=True)

#216 zjprookie opened 1 month ago
1
Bulk-ATAC-seq data - distal cis-regulatory elements annotation

#215 gosiagolda closed 2 months ago
0
ImportError: cannot import name 'default_motifs' from 'gimmemotifs.motif'

#214 chuyaowang opened 2 months ago
2
(Best practices) Is adding TF-target gene pairs manually required if I have generated the base_GRN from snATAC seq?

#213 yojetsharma opened 2 months ago
0
I am getting chekered plots upon running the links.plot function, how to correct this?

#212 yojetsharma closed 2 months ago
1
'ColormapRegistry' object has no attribute 'get_cmap'

#211 imraanGit opened 3 months ago
0
How to proceed if we don't have enough information to manually make a TF-target gene pair data?

#210 yojetsharma opened 3 months ago
0
Producing a video visualisation (like shown on https://celloracle.org/)

#209 jdarmitage opened 3 months ago
0
seuratToAnndata

#208 nhu-github opened 4 months ago
1
The Kernel crashed when I run tfi.scan

#207 Zhangruiqi111 opened 4 months ago
1
Error in calculating embedding shift

#206 Larrycpan closed 4 months ago
3
does not have enough regulatory connection in the GRNs. Cannot perform simulation.

#205 xiaomaolxc opened 4 months ago
0
Does celloracle need pseudotime information to give cluster wise GRNs?

#204 ruchikabhat opened 4 months ago
0
Saving plots as individual files?

#203 njrobins closed 5 months ago
2
GimmeMotifs installed but can't install celloracle because of 'Failed building wheel for gimmemotifs'

#202 jianwu1 opened 6 months ago
1
Can't convert from Seurat to anndata #8928

#201 xiaomaolxc closed 4 months ago
0
We don't have default motifs for your species, Please specify motif data by yourself.

#200 Roger-GOAT opened 6 months ago
1
Loading CellOracle takes too much time

#199 CYWu111 opened 6 months ago
0
Loading CellOracle takes too much time.

#198 xmuhuanglab closed 6 months ago
0
Heterogeneous dataset subsetting and number of cells/cluster

#197 acv21 opened 6 months ago
0
Fixed inconsistent results of `oracle.get_links` across runs

#196 PauBadiaM opened 6 months ago
0
model overfitting

#195 tkisss opened 7 months ago
0
Request for 3D UMAP

#194 fafa92 opened 7 months ago
0
Problem when using a custom genomes_dir for TF scan

#193 VictorCurean opened 7 months ago
2
Plot cell types under 'development' flow grid

#192 alexandrelanau opened 8 months ago
0
tfinfo and GRN files

#191 momur opened 8 months ago
4
WinError: FileNotFound at installation

#190 VictorCurean closed 7 months ago
1
Request for Schistosoma japonicum genome

#189 shycheng opened 8 months ago
0
editing the evaluate_and_plot_simulation_value_distribution function

#188 Alireza-Majd closed 8 months ago
1
tfi.scan error:

#187 Edsan17 closed 8 months ago
3
Building Base GRN with multiple samples

#186 shahrozeabbas opened 8 months ago
0
Vector Plots

#185 sarah-chapin opened 8 months ago
1
Projecting the simulated flows on a specific cluster

#184 jyang635 opened 8 months ago
1
Error with data_conversion.seurat_object_to_anndata

#183 JunyanKan closed 8 months ago
1
Adding new reference genome: Rn7

#182 MartijnLvandenBroek opened 9 months ago
0
Installation issue on Mac book pro/ VS Code

#181 jw235 opened 9 months ago
4
New genomes promoter_based_GRN

#180 dnjst opened 10 months ago
0
Problems with ma.get_tss_info function

#179 niklasbinder closed 10 months ago
3
TypeError: BaggingRegressor 'base_estimator'

#178 iichelhadi closed 10 months ago
4
Can we make custom genome annotation by custom gff and fasta file?

#177 duchen-whu opened 10 months ago
0
Question about edge filtering strategy of CellOracle

#176 R-Krait opened 10 months ago
0
Estimating cell density after perturbation

#175 jordiabante opened 10 months ago
0
The kernel keep dying during TF motif scan.

#174 Lukas20170 closed 10 months ago
1
How to check the available TF list in the oracle object

#173 YuchenXiangEMBL closed 8 months ago
1
Error with oracle.import_anndata_as_raw_count

#172 Hanxi-002 closed 8 months ago
1