digitalcytometry/ecotyper

Issues

• Tutorial 4 Discovery: I don't set Singularity but it seems tends to run on the Singularity, NOT the default Docker

  #84 opened a year ago by Sawakotx
  2

• Help with error Ecotyper failed: Error in RunJobQueue()

  #97 opened 5 months ago by WJRDW
  0

• Can EcoTyper be used in murine tumor analysis?

  #96 opened 5 months ago by Lewisen-Liu
  0

• How can I solve this issue?

  #87 opened 7 months ago by LynnChan99
  7

• Ecotyper website server

  #92 opened 7 months ago by bplet01
  4

• Running bulk recovery with published cell states

  #94 opened 7 months ago by WJRDW
  1

• errors with EcoTyper_recovery_bulk.R

  #86 opened 7 months ago by tjogzt
  2

• EcoTyper_recovery_bulk.R

  #83 opened 7 months ago by chrismahony
  3

• Discovery/recovery function & functional states like CancerSEA

  #90 opened 7 months ago by LiuCanidk
  1

• EcoTyper failed - EcoTyper_recovery_bulk.R

  #93 opened 7 months ago by AimSchina
  1

• Can it use in Non-tumor anlysis?

  #95 opened 7 months ago by fengqlin
  1

• ecotyper for GeoMx

  #82 opened 7 months ago by chrispatsalis
  1

• about Token of CIBERSORTx

  #81 opened 7 months ago by BolinLiuu
  1

• Question with TCGA cell state assignment from ecotyper website

  #79 opened 7 months ago by WuRAFY
  1

• Tutorial 3 error parse_args_output

  #78 opened 7 months ago by Torti11
  1

• tutorial 3 errors unless "Recovery cell type fractions" specified

  #77 opened 7 months ago by istvankleijn
  2

• Change the Size of Output Images?

  #70 opened 7 months ago by dmiyagi
  1

• Question regarding data displayed as heatmap on "https://ecotyper.stanford.edu/carcinoma/"

  #91 opened 8 months ago by itigupta2429
  0

• Spot-Level Immune Cell Deconvolution in Spatial RNA-seq Data

  #89 opened 9 months ago by sallyseullee-0821
  0

• [Ecotyper] Error in NMF step at Tutorial1 using user-defined profile

  #88 opened 10 months ago by jpark27
  1

• CIBERSORTx integration fails

  #49 opened 2 years ago by NoahHenrikKleinschmidt
  7

• Question about recovery scRNA in ecotyper

  #85 opened a year ago by LynnChan99
  0

• Failure of Recovery of Ecotypes (Tutorial 3) in Spatial Transcriptomics data

  #80 opened a year ago by corecontingency
  2

• Can't align to any ecotype

  #75 opened a year ago by WangKang-Leo
  1

• Error in consensus + nrun(x) * consensus(x) : non-conformable arrays

  #74 opened a year ago by WangKang-Leo
  2

• Will the marker gene vary with different discovery datasets?

  #73 opened a year ago by LynnChan99
  6

• Error: failed to create symbolic link 'datasets/bulk/bulk_lung_data/data.txt': Operation not permitted

  #72 opened a year ago by wanglu2014
  1

• cp: Cannot stat

  #71 opened a year ago by dmiyagi
  2

• step4 error

  #68 opened a year ago by sayhello854123
  6

• Step4 Errors in EcoTyper_discovery_scRNA.R

  #76 opened a year ago by WangKang-Leo
  0

• Metadata problem

  #69 opened a year ago by dmiyagi
  1

• Using an existing cancer single-cell atlas dataset as discovery?

  #67 opened 2 years ago by WangKang-Leo
  1

• How to get the cibersortx token?

  #66 opened 2 years ago by dufeng311
  1

• Problems downloading the results

  #64 opened 2 years ago by fernangomezv
  2

• question in recovery of cell states in scRNA dataset

  #65 opened 2 years ago by dufeng311
  2

• Issue with cell type specific genes when performing scRNAseq discovery

  #63 opened 2 years ago by dkwon6
  1

• Estimating cell-type fractions from bulk RNA

  #62 opened 2 years ago by danieljrichard
  1

• Dependency unmentioned in README

  #61 opened 2 years ago by SyouTono242
  1

• Ecotype run error

  #60 opened 2 years ago by Panyitong
  1

• genes used in input file

  #59 opened 2 years ago by mao223
  1

• Question: Discovery of ecotypes in bulk vs single-cell RNA

  #57 opened 2 years ago by ccruizm
  1

• Wilcoxon-error when having only a single cell

  #56 opened 2 years ago by NoahHenrikKleinschmidt
  1

• Error in tutorial 1

  #58 opened 2 years ago by mao223
  1

• Incongruence in Ecotype_Heatmap.pdf, Ecotype_Assignment.txt, and Ecotype_Abundance.txt sample number

  #54 opened 2 years ago by auroramaurizio
  1

• Turoial3: Visium tutorial

  #55 opened 2 years ago by chrismahony
  1

• Expression matrix of scRNA-seq

  #53 opened 2 years ago by HengqiLiu
  1

• question regarding abundance table

  #51 opened 2 years ago by kaizen89
  3

• Minimum coverage of bulk RNASeq samples for Lymphoma EcoTyper

  #52 opened 2 years ago by auroramaurizio
  1

• scRNA-Seq Lymphoma Recovery

  #50 opened 2 years ago by LeonHafner
  1

• Is the concept of ecotype suitable for chronic diseases?

  #48 opened 2 years ago by PiaoyangGuohai1
  1