immunogenomics/harmony

Issues

• Cannot reproduce Seurat.ipynb vignette; parameters not passed

  #243 opened 9 months ago by Nichal123
  4

• do_scatter is defined in the vignette source code but not available

  #260 opened 17 days ago by MichaelJFlynn
  1

• Trying to load pbmc.RData from Zenodo

  #248 opened 17 days ago by davetang
  2

• how to use harmony for Seurat Spatial Data?

  #254 opened 4 months ago by flpxn7
  1

• The error of harmony after subsetting data

  #256 opened 3 months ago by Carrey14
  2

• Typo in detailed walkthrough?

  #264 opened 19 days ago by dariober
  0

• Error: matrix multiplication: incompatible matrix dimensions: 100x96490 and 96489x22

  #237 opened 10 months ago by claireanjou
  3

• Best Practices for Sequential vs. Parallel Regression of Multiple Covariates in Harmony

  #263 opened 24 days ago by vertesy
  0

• Is Regressing Covariates in Both ScaleData and RunHarmony Redundant and Potentially Problematic?

  #262 opened 24 days ago by vertesy
  0

• Harmony converged after 6 iterations Error in UseMethod(generic = "Key", object = object) : no applicable method for 'Key'...

  #221 opened a year ago by ncedi12
  5

• Gene-level Correction

  #252 opened 5 months ago by DarioS
  0

• argument 3 matches multiple formal arguments

  #253 opened a month ago by jasoncrucify
  4

• argument 3 matches multiple formal arguments

  #255 opened a month ago by Guliariel
  1

• integrating snRNA (from multiome dataset) with scRNA public dataset

  #258 opened 3 months ago by Urja25
  1

• different clustering results

  #259 opened 3 months ago by pikapika505
  1

• "Is It Feasible to Use Harmony Directly for Batch Correction in Seurat V5 Instead of “ IntegrateLayers“?"

  #249 opened 7 months ago by Tylesteven
  5

• advice about parameters for integration

  #251 opened 6 months ago by javiers1983
  0

• Can i obtain my original data shape?

  #247 opened 9 months ago by leeleavitt
  3

• Harmony using a predefined clustering vector

  #250 opened 7 months ago by tkcaccia
  5

• Reordering PCs?

  #245 opened 7 months ago by yesitsjess
  1

• Is it okay to paste two covariates into one when correcting for two covariates?

  #246 opened 8 months ago by YiweiNiu
  4

• RunHarmony on the weights branch errors with incompatible matrix dimensions

  #219 opened a year ago by deevdevil88
  16

• Integration of scATACseq datasets

  #244 opened 9 months ago by pobmmu
  1

• Convergence plot showing bizarre reading, data okay to use?

  #241 opened 9 months ago by jcshuy
  2

• vars_use Definition Not Explicit

  #242 opened 9 months ago by DarioS
  0

• No Instructions for Tissues and Cell Culture Merging

  #240 opened 9 months ago by DarioS
  6

• Plotting Function do_scatter Does Not Exist

  #239 opened 10 months ago by DarioS
  1

• feature.loadings of harmony is missing in SummarizedExperiment

  #238 opened 10 months ago by xiangpin
  0

• Differential expression and volcano

  #236 opened 10 months ago by antoine4ucsd
  4

• Installation issue MacOS Monterey

  #213 opened a year ago by SalimMegat
  8

• How do I download version 0.99.9 of harmony?

  #235 opened a year ago by Yuan-9
  20

• Lambda selection

  #232 opened a year ago by erflynn
  6

• Merging or Combining multiple ArchRProject Objects

  #233 opened a year ago by qdong2023
  1

• How to combine/merge three ArchRProject objects

  #229 opened a year ago by qdong2023
  2

• error when integrate multiple layers' batches

  #231 opened a year ago by hanst716
  1

• installation issues

  #217 opened a year ago by vappiah
  3

• harmony performance eval

  #225 opened a year ago by antoine4ucsd
  4

• Integration of patient-matched tumor and normal tissue samples

  #230 opened a year ago by samgest
  3

• Error in harmony

  #228 opened a year ago by ydai3
  3

• Error in RunHarmony: argument 3 matches multiple formal arguments

  #227 opened a year ago by katimbach
  2

• Installation issues

  #226 opened a year ago by ayyildizd
  2

• harmony for normalized scRNA-seq dataset

  #224 opened a year ago by martina811
  1

• Batch effect seen on Heatmap

  #216 opened a year ago by Lucas-Maciel
  5

• New version does not respect `verbose = FALSE`

  #211 opened a year ago by const-ae
  2

• question regarding harmony elbow plot and PCs selection

  #222 opened a year ago by iichelhadi
  5

• mutiple covariates - error number of lambdas specified

  #223 opened a year ago by antoine4ucsd
  2

• Parameters for integrating different species

  #220 opened a year ago by DiracZhu1998
  5

• Simple harmony call fails on v1.1.0

  #214 opened a year ago by const-ae
  5

• harmony::RunHarmony v1.1.0 ignoring parameters

  #215 opened a year ago by jcshuy
  1

• conda install -c bioconda r-harmony failed

  #210 opened a year ago by hanguojun007
  1