neurogenomics/MAGMA_Celltyping

Issues

• map_snps_to_genes() related error

  #145 opened a year ago by barbareyex
  4

• map_snps_to_genes() and get_ctd() related errors

  #149 opened 4 months ago by zsf123525
  1

• found 0 valid gene covariates, for 0 genes defined in genotype data

  #147 opened 8 months ago by sanderslhc
  11

• Magma used in other species

  #148 opened 8 months ago by sanderslhc
  1

• Parallelise MAGMA steps

  #110 opened 2 years ago by bschilder
  1

• too many correlations

  #146 opened 9 months ago by sanderslhc
  0

• ERROR - reading gene covariate file: duplicate covariate variable name

  #142 opened a year ago by bschilder
  3

• `map_snps_to_genes`: Handle bgzipped files

  #144 opened a year ago by bschilder
  1

• Assess whether MAGMA can take multi-allelic SNPs

  #143 opened a year ago by bschilder
  13

• *gsa.out: truncated `VARIABLE` names

  #141 opened a year ago by bschilder
  1

• Create CTDs from `scRNAseq` package datasets

  #119 opened 2 years ago by bschilder
  0

• Unable to import the example GWAS summary statistics when MUNGE = FALSE

  #136 opened 2 years ago by Sheenlei
  1

• Issue in EWCE if I leave MAGMA.Celltyping calculate the quantiles

  #122 opened a year ago by AMCalejandro
  1

• WARNING: 228 columns (cell-types) have less than the expected number of quantile bins (10).

  #125 opened a year ago by AMCalejandro
  1

• Fix GH Actions

  #120 opened a year ago by bschilder
  2

• Problem with zeisel 2018 ctd

  #130 opened a year ago by KittyMurphy
  1

• get_ctd doesn't work - "missing token error"

  #140 opened a year ago by the-confused-scientist
  1

• MAGMA.Celltyping::import_magma_files issue

  #137 opened 2 years ago by sofiapuvogelvittini
  1

• Maybe allow user to decide on how to adjust

  #134 opened 2 years ago by AMCalejandro
  2

• Bug report:Error in if (is.null(N) | is.na(N)) { : argument is of length zero

  #128 opened a year ago by ZhengGongwei
  4

• Likely bug if dendro is set to Null

  #127 opened a year ago by AMCalejandro
  1

• magma_tileplot does not overlap the dendrogram with the heatmap

  #126 opened a year ago by AMCalejandro
  2

• Overadjustment for multiple testing?

  #123 opened a year ago by AMCalejandro
  2

• ERROR - configuration: unknown modifier 'twosided' for flag --set-annot

  #129 opened a year ago by AMCalejandro
  1

• Add functions to import genes.out and genes.raw files into R

  #109 opened a year ago by bschilder
  2

• `\doi{}` tag not rendering properly

  #139 opened a year ago by bschilder
  0

• Add full AIBS data from all regions

  #138 opened a year ago by bschilder
  1

• Almost all CTDs are not available

  #131 opened 2 years ago by AMCalejandro
  3

• Unable to pass path to refen

  #124 opened 2 years ago by AMCalejandro
  0

• Error running after using new version of .rds files

  #107 opened 2 years ago by Captain-Pam
  4

• Upload Zeisel2018 CTD

  #118 opened 2 years ago by bschilder
  0

• Automatically infer species from genes when `ctd_species=NULL`

  #117 opened 2 years ago by bschilder
  0

• `get_driver_genes`: select genes by mean rank

  #116 opened 2 years ago by bschilder
  0

• `merge_results`: create`save_dir` if not already present

  #115 opened 2 years ago by bschilder
  0

• Use `adjust_zstat_in_genesOut` without a CTD

  #114 opened 2 years ago by bschilder
  1

• conditional `calculate_celltype_associations`: `ERROR - reading gene covariate file: duplicate gene entry`

  #113 opened 2 years ago by bschilder
  2

• `map_snps_to_genes`: Add *--genes-only* arg

  #108 opened 2 years ago by bschilder
  1

• `magma_tileplot`: `rror in q < 1e-05 : comparison (3) is possible only for atomic and list types`

  #112 opened 2 years ago by bschilder
  1

• Update `full_workflow` vignette to work

  #111 opened 2 years ago by bschilder
  0

• `get_ctd`:`Error in gzfile(file) : invalid 'description' argument`

  #106 opened 2 years ago by bschilder
  0

• Add Tabula Muris

  #104 opened 2 years ago by bschilder
  0

• Installation failed

  #98 opened 2 years ago by XihanZhang
  4

• get_genomeLocFile() issue

  #102 opened 2 years ago by shivani-raja
  8

• Error in "map_snps_to_genes"

  #105 opened 2 years ago by LDHHAHA
  8

• get_genomeLocFile error

  #100 opened 2 years ago by malosreet
  6

• MAGMA_Files_Public studies identification

  #103 opened 2 years ago by sofiapuvogelvittini
  1

• Problem with get_genomeLocFile

  #101 opened 2 years ago by malosreet
  1

• time out 300s

  #99 opened 2 years ago by Thinknoon
  4

• cell type data no longer compatible with EWCE

  #97 opened 2 years ago by roxyisat-rex
  3

• Compare `MAGMA.Celltyping` v1.0 vs. v2.0

  #96 opened 2 years ago by bschilder
  0