pinellolab/dictys

Issues

• NaN's arise in dictys.network.reconstruct

  #66 opened 3 months ago by ekernf01
  2

• creating with "data/coord_rna.tsv.gz"

  #65 opened 4 months ago by OneHitKO
  3

• Mathematical description of indirect effects

  #61 opened 4 months ago by ekernf01
  5

• RuntimeError: No motif found.

  #63 opened 5 months ago by nikithkurella
  8

• PermissionError: [Errno 13] Permission denied: 'analysis-blood.tar.xz'

  #64 opened 4 months ago by zly19980908
  2

• Integration of bulk ATAC-seq data and scRNAa-seq data: what is the "w" in the "PositionID"?

  #62 opened 4 months ago by kamisama0101
  3

• errors running full human multiome

  #58 opened 5 months ago by hshcao
  3

• Data input type

  #23 opened a year ago by orbitalse
  5

• Dynamic inference errors using custom subsets

  #59 opened 6 months ago by nikithkurella
  8

• ERROR when running 2.1 GPU part, execution

  #56 opened 6 months ago by siduanmiao
  7

• Dynamic inference with existing pseudotime values

  #54 opened 6 months ago by nikithkurella
  4

• errors running 1.1 CPU part 1, execution

  #57 opened 6 months ago by hshcao
  0

• ValueError: <10 TFs found in motifs.motif file.

  #53 opened 8 months ago by nikithkurella
  3

• dictys_helper

  #51 opened 8 months ago by nikithkurella
  4

• human hematopoiesis

  #52 opened 8 months ago by master-XS
  1

• network strength

  #50 opened 9 months ago by Trafalgar-ROOM
  2

• Creating .h5 output file

  #49 opened 10 months ago by e-arslan
  1

• ChIP-seq datasets from Cistrome database and ChIP-seq + HiC results for evaluation

  #48 opened 10 months ago by Zengggg
  1

• Can I run dictys only on single-cell data?

  #42 opened 10 months ago by SMU-TK-2022
  1

• Can I integrate my own scRNA-seq data and bulk ATAC-seq data?

  #46 opened a year ago by 13021969200
  5

• Error when running STREAM trajectory inference on co-embedded data (following in the full-skin tutorial)

  #47 opened a year ago by HarrisHan2k
  1

• Four multiome samples, 2 different treatment conditions

  #45 opened a year ago by kfenggg
  1

• How to use separate scRNA-seq and scATAC-seq data to Create dynamic GRN ?

  #36 opened a year ago by thinkingpeach-z
  2

• The number of obtained marker genes is very low.

  #40 opened a year ago by bioinformaticspcj
  1

• Problem with custom installation

  #39 opened a year ago by j3gu
  3

• Run bulk ATAC-seq data failed!!!

  #37 opened a year ago by bioinformaticspcj
  5

• Run bulk ATAC-seq data failed

  #38 opened a year ago by bioinformaticspcj
  0

• How to use Bulk ATAC to Run

  #28 opened a year ago by hzauleibowen
  18

• How to access to trajectory and expression data for benchmarking

  #29 opened a year ago by nathanmaulding
  14

• Is it possible to use fragment files as input? How to dictys for multiple samples?

  #33 opened a year ago by xgaoo
  3

• Using Dictys in mosaic data

  #25 opened a year ago by ccruizm
  10

• Suggestions to reduce storage ？？？

  #35 opened a year ago by bitcometz
  3

• where I can find update-makefile-variables.py?

  #34 opened a year ago by bitcometz
  1

• Preparation of input data

  #31 opened a year ago by YoonheeJ
  2

• Running Dictys makefile static.mk

  #24 opened a year ago by sureshsatpati
  21

• Use of v10nr_clust_public in SCENIC+

  #26 opened a year ago by pchiang5
  14

• ValueError: Subset RNA cells not found in population

  #27 opened a year ago by orbitalse
  2

• Other motifs from other motif database?

  #22 opened a year ago by willey2020
  2

• dynamic regulatory strength plot(with pseudotime)

  #21 opened a year ago by willey2020
  2

• Threads vs. Jobs

  #20 opened 2 years ago by JBreunig
  2

• I have an analysis with another tool (e.g. Signac), can I still use dictys？

  #19 opened 2 years ago by LalicJ
  2

• Doubt about a claim made in the paper

  #17 opened 2 years ago by cakeinspace
  8

• Help with saving figures

  #15 opened 2 years ago by JasonOSS
  1

• tmp_dynamic required for analysis ?

  #14 opened 2 years ago by JasonOSS
  1

• datasets input as scATAC only

  #12 opened 2 years ago by willey2020
  4

• Help with makefiles parameters

  #11 opened 2 years ago by JasonOSS
  2

• How to run Dictys from aggregated samples ?

  #10 opened 2 years ago by JasonOSS
  2

• issue while running network inference step

  #5 opened 2 years ago by sid5427
  3

• Can't update config.mk in the "2-makefile" notebook

  #9 opened 2 years ago by JasonOSS
  11

• Can I run dictys with 10X multiome?

  #4 opened 2 years ago by massonix
  8