hbctraining/scRNA-seq_online

Issues

• harmony advanced vignette link broken

  #124 opened 2 months ago by Gammerdinger
  0

• Add packages

  #123 opened 2 months ago by Gammerdinger
  1

• Typo in image

  #122 opened 2 months ago by Gammerdinger
  0

• Update homework

  #121 opened 4 months ago by nsohail19
  0

• Trouble downloading ' scRNA-seq filtered counts' from the Pseudobulk DEG analysis tutorial

  #118 opened 4 months ago by yeseul830
  4

• Decision tree?

  #90 opened 5 months ago by eberdan
  3

• doublet detection tools

  #94 opened 5 months ago by rkhetani
  0

• add an image to represent the Seurat object

  #120 opened 5 months ago by mistrm82
  1

• Regressing out cell cycle scores on SCTransform work-flow

  #73 opened 5 months ago by camelest
  0

• update some of the visualizations

  #111 opened 5 months ago by mistrm82
  0

• Using SCT for marker ID

  #96 opened 5 months ago by rkhetani
  3

• Normalization at various steps

  #97 opened 5 months ago by rkhetani
  5

• update links in "Resources"

  #104 opened 5 months ago by mistrm82
  1

• v5 issue with GetAssay()

  #114 opened 5 months ago by mistrm82
  1

• Quality Control visualizations

  #110 opened 5 months ago by chenqing1991
  1

• cycle.rda file missing

  #115 opened 5 months ago by ChrisSteel-bio
  1

• Pseudobulk functionality within Seurat

  #116 opened 8 months ago by pipes82
  1

• PCA and elbow plot

  #117 opened 7 months ago by ptranvan
  0

• many to many warning when assigning annotations to markers in scRNAseq

  #112 opened a year ago by hwick
  0

• 08 clustering qc errors

  #109 opened a year ago by hwick
  2

• cell cycle scoring may need updates

  #107 opened a year ago by hwick
  2

• cell cycle phase in seurat_integrated isn't kept?

  #108 opened a year ago by hwick
  1

• redundant code

  #103 opened a year ago by mistrm82
  1

• more challenging exercises

  #106 opened a year ago by mistrm82
  0

• Add materials on troubleshooting

  #105 opened a year ago by mistrm82
  0

• Error in theory of PCA

  #100 opened a year ago by hortensebst
  1

• DESeq2 normalization

  #102 opened a year ago by jc271828
  3

• add code for unintegrated UMAP

  #95 opened a year ago by mistrm82
  1

• set seed at the start of the workshop

  #98 opened a year ago by rkhetani
  1

• obtaining raw data for the tutorial (lesson 03 SC quality control setup)

  #99 opened a year ago by obalasz
  1

• Matrix.utils package (used in pseudobulk DEA lesson) is archived from CRAN

  #101 opened a year ago by Amelie-TGHN
  0

• using "v2" for SCTransform

  #89 opened 2 years ago by mistrm82
  2

• Update all links for project download

  #93 opened 2 years ago by mistrm82
  0

• Issues with the scRNAseq workshop material and my own data - integration

  #91 opened 2 years ago by Hannah-Doerpholz
  6

• simplifying SCTransform explanation

  #69 opened 2 years ago by mistrm82
  1

• new version of scTransform released!

  #78 opened 2 years ago by pipes82
  3

• adding a note on Harmony

  #85 opened 2 years ago by mistrm82
  1

• Remove SingleCellExperiment package

  #66 opened 2 years ago by jihe-liu
  0

• Difference between normalizeData() and SCTransform()

  #67 opened 2 years ago by rkhetani
  1

• Reference for pseudobulk approach for DE analysis

  #68 opened 2 years ago by marypiper
  2

• updating the lesson goals, challenges, recommendations

  #71 opened 3 years ago by mistrm82
  0

• break down clustering explanation

  #72 opened 2 years ago by mistrm82
  1

• link broken in pseudobulk lesson

  #83 opened 2 years ago by mistrm82
  0

• pseudobulk DE paired design

  #84 opened 2 years ago by mistrm82
  0

• Missing file in scRNA-seq analysis -> Downstream Analysis -> Differential Expression Between Conditions

  #80 opened 2 years ago by singhh5050
  2

• Confused about using "sum" for pseudobulk DESeq2

  #74 opened 3 years ago by Famingzhao
  1

• split_seurat.rds dataset was out of data

  #77 opened 3 years ago by JiaqiHu2021
  2

• single_cell_rnaseq.zip no longer available on Dropbox

  #79 opened 3 years ago by rbatorsky
  4

• shuffling order of QC metrics

  #70 opened 3 years ago by mistrm82
  1

• next dataset for revamping workshop

  #62 opened 3 years ago by marypiper
  0