Functional-Genomics/eQTL

Issues

• flanking option passed to other scripts

  #31 opened 8 years ago by clody23
  1

• change line 159 dna.mk

  #32 opened 8 years ago by clody23
  1

• issue with multiple test correction with cis qtl

  #30 opened 8 years ago by clody23
  0

• change sorting of pheno and geno

  #24 opened 8 years ago by clody23
  0

• print more informative messages in sort_ids.py

  #29 opened 8 years ago by clody23
  0

• filter columns based on DNA- RNA matched columns also on covariates file

  #25 opened 8 years ago by clody23
  1

• Fix the beta

  #23 opened 8 years ago by nunofonseca
  2

• fix the filter_columns.R problem with MEM :-P

  #28 opened 8 years ago by clody23
  2

• check if the bcftoosl merging of merged somatic vcfs is working although they don't have genotypes

  #27 opened 8 years ago by clody23
  1

• no float in the var_name of the summary file

  #26 opened 8 years ago by clody23
  0

• qq-plots

  #9 opened 9 years ago by clody23
  2

• add option to the make file to filter chromosomes also on the phenotype matrix

  #21 opened 9 years ago by clody23
  1

• output also strand in the gtf annotation

  #22 opened 9 years ago by clody23
  3

• do not compute correlation with clustering of kinship matrix

  #20 opened 9 years ago by clody23
  1

• set just one type of samples cutoff value throughout the pipeline

  #19 opened 9 years ago by clody23
  0

• sample name in mtql pipline

  #18 opened 9 years ago by clody23
  0

• handle error if summary.hdf5 file generated by eqtl_summary.py is an empty file

  #13 opened 9 years ago by clody23
  0

• select genes from phenotype matrix based on chromosomes

  #12 opened 9 years ago by clody23
  1

• changes into the make file to support quantile normalisation

  #17 opened 9 years ago by clody23
  0

• 2 = homozygous reference due to plink?

  #14 opened 9 years ago by clody23
  1

• output study size in the settings.tsv file

  #16 opened 9 years ago by clody23
  1

• aggregate somatic events by genomic region

  #15 opened 9 years ago by clody23
  1

• Compute empirical p-values

  #7 opened 9 years ago by nunofonseca
  1

• add a column to the summary file for empirical pvalues: if n_perm = 1 then put NaN

  #11 opened 9 years ago by clody23
  1

• do not allocate memory for matrix with permuted pvalues for cis

  #10 opened 9 years ago by clody23
  0

• modify the R script to do the hclustering to check if matrix has NaN

  #8 opened 9 years ago by clody23
  1

• Avoid hardcoding a blacklist of chr

  #4 opened 9 years ago by nunofonseca
  0

• chr data type should not be a float

  #3 opened 9 years ago by nunofonseca
  0

• Covariate file can be empty?

  #5 opened 9 years ago by nunofonseca
  1

• Create a empty kpop

  #6 opened 9 years ago by nunofonseca
  1

• Do not start the analysis if the mac value is greater than the number of samples

  #2 opened 9 years ago by nunofonseca
  0

• Heatmap/PCA colours

  #1 opened 9 years ago by clody23
  1