Durenlab/LINGER

Issues

• General Human GRN Not Accessible

  #59 opened in 4 hours by borcuttjahns
  0

• Issue with preprocess

  #53 opened 2 months ago by danielcgingerich
  1

• Reproducibility of Supplementary Table 7

  #57 opened 12 days ago by Zengggg
  0

• TF_RE_binding

  #58 opened 11 days ago by danielcgingerich
  0

• Mismatching error in sp.vstack([adata_RNA.X.T, adata_ATAC.X.T]) among my ATAC and RNA.h5ad files

  #52 opened 25 days ago by yojetsharma
  0

• How should we interpret the output results?

  #56 opened a month ago by Therabbiteating
  0

• Creation of Fig.5f?

  #55 opened a month ago by yojetsharma
  0

• Run LINGER on subset of genes

  #54 opened 2 months ago by danielcgingerich
  0

• how does LINGER work on bulkRNA only?

  #39 opened 5 months ago by zhumo-111
  1

• will LINGER work on unpaired scRNA-seq and scATAC-seq data?

  #29 opened 7 months ago by qiuhuiqq
  3

• FileNotFoundError: [Errno 2] No such file or directory: 'chr1_cell_population_TF_RE_binding.txt'

  #49 opened 2 months ago by jessicaliu09
  7

• AttributeError: module 'LingerGRN.LINGER_tr' has no attribute 'RE_TG_dis'

  #44 opened 2 months ago by XiaoKaixuan12333
  1

• cell type specific gene regulatory network

  #34 opened 6 months ago by leonardHerault
  2

• Error of cell_type_specific_TF_RE_binding_chr() function

  #38 opened 5 months ago by xiaoxiao6630
  2

• FileNotFoundError: chr1_cell_population_TF_RE_binding.txt'

  #42 opened 4 months ago by ayavuzcakir
  4

• No such file or directory: '/home/data6/zhangruiqi/LINGER/output/Symbol.txt'

  #50 opened 2 months ago by Zhangruiqi111
  1

• loading and running multiple samples .h5 files as an input?

  #51 opened 2 months ago by yojetsharma
  0

• error in LINGER_tr.training

  #40 opened 4 months ago by feanaros
  2

• Source code

  #48 opened 2 months ago by mbensouda
  2

• Benchmark TF-RE linkage

  #28 opened 7 months ago by Cai-fx
  3

• trans-regulatory network

  #45 opened 3 months ago by MoLuLuMo
  2

• gpu support?

  #33 opened 6 months ago by RubenVanEsch
  1

• How to run LINGER without creating pseudo-bulk or metacell?

  #47 opened 3 months ago by lzj1769
  0

• Error: elementwise comparison failed; while running LL_net.cell_type_specific_TF_RE_binding(GRNdir,adata_RNA,adata_ATAC,genome, celltype,outdir,method)

  #46 opened 3 months ago by karamveerverma37
  0

• How to use homer to get the TF-RE binding score matrix?

  #43 opened 4 months ago by FengAoWang
  0

• The feasibility of using a gene regulatory network (GRN) inferred from healthy human kidneys to calculate transcription factor (TF) activity in TCGA data for clear cell renal cell carcinoma (ccRCC) tumor and normal samples, as well as in scRNA-seq data of ccRCC, can be assessed as follows

  #41 opened 4 months ago by qsk0425
  0

• can't find get_adata u

  #23 opened 7 months ago by LinLi-0909
  1

• Error Running PMBC example

  #37 opened 5 months ago by AlMuCan
  0

• The problem with downloading the 'data_bulk.tar.gz' file.

  #36 opened 5 months ago by qsk0425
  0

• Error in load_TFbinding()

  #32 opened 6 months ago by myylee
  2

• general gene regulatory network link not working with wget

  #31 opened 7 months ago by RubenVanEsch
  4

• Cell level trans-regulatory potential

  #22 opened 7 months ago by kmakino14
  1

• Reproducinility of FOXN1 activity in Figure 6b

  #26 opened 7 months ago by kmakino14
  1

• highly variable gene number

  #30 opened 7 months ago by xinghao-1210
  0

• there isn't find_neighbors()

  #21 opened 7 months ago by gaotai8
  6

• there is a question in GRN-infer.md

  #27 opened 7 months ago by gaotai8
  0

• About preprocess function

  #15 opened 7 months ago by kmakino14
  5

• Input raw counts or log-normalized data?

  #24 opened 7 months ago by kmakino14
  0

• genome error

  #20 opened 7 months ago by feanaros
  2

• there isn't get_adata and barcode_use

  #19 opened 7 months ago by gaotai8
  3

• i have resovlved this error,thanks!

  #18 opened 7 months ago by weishangxiao
  3

• Seurat dataset for LINGER

  #16 opened 7 months ago by feanaros
  6

• Request for Computational Resource Details for Replicating Study

  #17 opened 7 months ago by wahahaaaa123
  1