morris-lab/CellOracle

Issues

• More than 3000 genes

  #169 opened 6 months ago by sarah-chapin
  0

• About the benchmarking datasets

  #146 opened a year ago by Chen-Li-17
  3

• Is CellOracle suitable for analysing cross-organ development for the same cell type?@JiaGuangshuai

  #168 opened 6 months ago by kzxkzx
  0

• gene selection from loaded seurat object

  #167 opened 6 months ago by A-legac45
  2

• visualization error layout

  #166 opened 7 months ago by A-legac45
  1

• Cannot make plots after importing celloracle

  #160 opened 9 months ago by pavsol
  1

• oracle.suggest_mass_thresholds()

  #163 opened 8 months ago by yiqisu
  1

• Could you implement the genome of Parasteatoda tepidariorum as well, please?

  #165 opened 8 months ago by unaginekomoyashi
  0

• Is it possible to adjust the clustering information of all cells to the same value in order to investigate the feasibility of identifying regulons?

  #164 opened 8 months ago by liuzj039
  0

• ImportError: cannot import name 'default_motifs' from 'gimmemotifs.motif'

  #158 opened 9 months ago by acv21
  5

• Error in Oracle.get_Links

  #161 opened 8 months ago by debashish19211
  2

• CellOracle KO simulation produced results opposite to real KO results

  #162 opened 8 months ago by Sustella
  0

• could you please add available reference genome of Macaca

  #152 opened 10 months ago by chenc327
  4

• Can we annotate TSS using scATAC-seq datasets?

  #151 opened 10 months ago by yangjun9095
  1

• about simulated expression

  #159 opened 9 months ago by Lipxiao
  1

• TF Binding Motif Scan not consistently working

  #156 opened 9 months ago by scongrove
  1

• Problems with reference genome for construction of base GRN from scATAC data

  #125 opened a year ago by rickycolman
  5

• 30k genes were found in the adata. Note that Celloracle is intended to use around 1000-3000 genes, so the behavior with this number of genes may differ from what is expected.

  #157 opened 10 months ago by MariaRosariaNucera
  0

• error when loading oracle data

  #154 opened 10 months ago by heroineray
  1

• Please help with reproduing the zebrafish analysis

  #155 opened 10 months ago by bitcometz
  0

• Could you please provide the processed Zebrafish scRNA-seq data？

  #153 opened 10 months ago by bitcometz
  0

• How to process multiple Bulk ATAC-seq datasets?

  #135 opened a year ago by Crorazon
  2

• Is celloracle supporting any gene pertutation beside TF genes?

  #148 opened 10 months ago by bitcometz
  2

• Why does the miniconda directory live in `/root` in the docker image?

  #149 opened a year ago by DongzeHE
  2

• IndexError from get_links()

  #147 opened a year ago by mindproof24
  2

• plot_mc_results_as_kde error

  #145 opened a year ago by iwanorittks
  2

• Query: Prepare base GRN construction with ArchR

  #144 opened a year ago by ribogod
  1

• inferring cell types from markers instead of preassigned cell types

  #142 opened a year ago by janursa
  4

• Non-uniform simulate_shift

  #143 opened a year ago by aaposaav
  0

• Bug or common? How to find the parameters for n_grid and min_mass?

  #141 opened a year ago by Zhuang-Bio
  2

• Perturbation scores for individual cells.

  #136 opened a year ago by aaposaav
  2

• ImportError: dlopen: cannot load any more object with static TLS

  #138 opened a year ago by LJK1991
  2

• installation error

  #140 opened a year ago by heroineray
  2

• I want to know how to load data

  #139 opened a year ago by YuyaOsada
  0

• Docker pull command error

  #137 opened a year ago by dyl4nm4rsh4ll
  2

• Problems importing celloracle to python

  #133 opened a year ago by aaposaav
  2

• Error when pulling the latest docker image

  #130 opened a year ago by officialprofile
  1

• oracle.get_mcmc_cell_transition_table

  #134 opened a year ago by debashish19211
  0

• No convergence error

  #126 opened a year ago by Jokendo-collab
  4

• How to compare degree value of each gene between clusters?

  #132 opened a year ago by Roger-GOAT
  0

• install error

  #131 opened a year ago by smilesw
  1

• oracle.to_hdf5 killed the proccess

  #129 opened a year ago by DLGisch
  0

• Loading peaks.bed

  #128 opened a year ago by Jokendo-collab
  0

• List of top 30 genes from each centrality measure

  #127 opened a year ago by mtrebelo
  0

• Error in tfi.scan motif scan output - missing factors

  #121 opened a year ago by Mesi395
  2

• Request of Rice genome

  #124 opened a year ago by Lidw2020
  0

• https://celloracle.org is not accessible

  #122 opened a year ago by dburkhardt
  0

• Availability of tissue- or cell-type-specific ground-truth networks

  #123 opened a year ago by dburkhardt
  0

• oracle.import_TF_data(TF_info_matrix=base_GRN) doesn't find overlap between base GRN and my scRNAseq data

  #120 opened a year ago by lpuche
  1

• Problem intiating CellOralce object due to colorbar

  #119 opened a year ago by degrainger
  0