neurorestore/Libra

Issues

• Error in `$<-.data.frame`(`*tmp*`, "replicate", value = integer(0))

  #55 opened 3 months ago by yuanG2000
  6

• Is it possible to add pct.1 / pct.2 column in the result?

  #54 opened 4 months ago by jamesbangbang1126
  1

• Question about batch effect correction

  #56 opened 2 months ago by 1226235
  1

• How to correct for age, sex, etc.?

  #52 opened 4 months ago by yesitsjess
  1

• Mixed model methods retuning only one cell type.

  #53 opened 4 months ago by brianherb
  1

• Error: Column `cell_type` is not found

  #51 opened 5 months ago by jamesonholloman
  5

• The dataset used for the demonstration `hagai_toy` reported an error

  #50 opened 6 months ago by Taoo777
  3

• Error in (function (cl, name, valueClass) : "data" is not a slot in the "Assay5" category.

  #49 opened 7 months ago by Pigeongeon
  3

• “Column `cell_type` is not found.”

  #46 opened 9 months ago by ltj-github
  3

• Reference level of `label_col` factor not respected

  #48 opened 7 months ago by agrier-wcm
  1

• How to perform edgeR-LRT using Libra with no biological replicates?

  #30 opened 2 years ago by DrDaedalusWHU
  2

• All p.val are N.A. for mixedmodel

  #45 opened 8 months ago by DelongZHOU
  2

• How to determine two comparison groups

  #47 opened 9 months ago by yanwuanxin
  0

• Something about the delay

  #44 opened 10 months ago by JianSongHuang
  0

• edgeR analysis not preserving the level and order information of the Cell_type

  #21 opened 2 years ago by RobertWhitener
  5

• Error when no cells present in one condition cell type

  #43 opened a year ago by mhvbyrne
  0

• Issue of avg_logFC in pseudobulk RNA seq output file

  #42 opened a year ago by jujurring
  3

• input of run_de function when using a Seurat object

  #37 opened a year ago by pandaqiuqiu
  10

• A quick question about application of liner mixed model method to detect degs

  #41 opened a year ago by HelloWorldLTY
  7

• Column `cell_type` is not found.

  #9 opened 2 years ago by fredust
  16

• Design order and account batch effect

  #32 opened 2 years ago by VergaJU
  8

• Error in `group_by()`: Column `cell_type` is not found.

  #14 opened 2 years ago by sshakil12
  10

• NA values when using mixedmodel for deg identificaiton.

  #40 opened a year ago by HelloWorldLTY
  0

• Some questions about mixed model

  #39 opened a year ago by HelloWorldLTY
  2

• How to generate the pseudobulk datasets in this paper?

  #38 opened a year ago by HelloWorldLTY
  4

• run_de function is not found.

  #36 opened 2 years ago by elifozcelik
  4

• 2 bulk_rnaseq datasets on Zenodo are missing

  #35 opened 2 years ago by Nayrouz109
  1

• Can we speed up run_de with mixed models ?

  #34 opened 2 years ago by Nayrouz109
  2

• How to get a relative high confidence results in the circumstance of using a imbalanced data

  #33 opened 2 years ago by thecatgonewithwid
  1

• min_feature option in run_de not working

  #29 opened 2 years ago by Peter-bbh
  7

• Some Thing Wrong with DESeq2 and Limma?

  #31 opened 2 years ago by hjh-air-cond
  4

• Could not find function "run_de"

  #24 opened 2 years ago by venchi9
  6

• Feature request: percentage expressed

  #28 opened 2 years ago by GBeattie
  1

• Replication, Label, and Cell Type for DEG

  #27 opened 2 years ago by Sayyam-Shah
  4

• Just wanna be sure about the result.

  #26 opened 2 years ago by hjh-air-cond
  2

• Accounting for covariates

  #25 opened 2 years ago by smorabit
  2

• Libra - singlecell giving opposite results

  #23 opened 2 years ago by saisomesh2594
  1

• What is 'label' and 'replication' in my single-cell datasets?

  #22 opened 2 years ago by victorwang123
  1

• Keeping the Gene names when calculating delta Variance

  #20 opened 2 years ago by RobertWhitener
  2

• Application of Libra to my dataset

  #19 opened 2 years ago by RobertWhitener
  2

• I change the param in edgeR-LRT, and get a better result.

  #18 opened 2 years ago by huanananan
  1

• limma not working correctly

  #17 opened 2 years ago by chengmingbo
  2

• cell_type not found when subsetting object

  #15 opened 2 years ago by MjelleLab
  2

• Differential expression on genes detected in min number of cells

  #16 opened 2 years ago by sshakil12
  1

• Can Libra be used in other setting?

  #13 opened 2 years ago by favilaco
  4

• Error in extract(., , meta0$cell_barcode)

  #12 opened 2 years ago by sshakil12
  2

• limma trend and voom

  #11 opened 2 years ago by alikhuseynov
  2

• cell_type not found

  #7 opened 2 years ago by Jeron1996
  6

• Genes with same adj p-val, p-val and log FC?

  #10 opened 2 years ago by anjkris
  1

• cell_type not found for example dataset from Zenodo

  #8 opened 3 years ago by stanleyjs
  1