natsuhiko/rasqual

Issues

• Problems with multiple definitions of certain header files during configuration during installation

  #60 opened 3 months ago by atw520
  0

• Compiling requires `-fcommon` flag on GCC v10+

  #59 opened 4 months ago by austintwang
  1

• potential bug in pasteFiles

  #58 opened 7 months ago by xfanhuang
  0

• Z-score or effect and standard error

  #55 opened 3 years ago by plbngl
  4

• qvalue nan error

  #11 opened 6 years ago by girdhar3
  4

• Library size factor from DESeq2 as Offset

  #57 opened 2 years ago by KRSBar
  0

• ASVCF version

  #56 opened 3 years ago by plbngl
  1

• fSNP not tested?

  #53 opened 3 years ago by plantformatics
  0

• Number of fSNP is 0 but lead QTL within peak

  #52 opened 3 years ago by Zepeng-Mu
  0

• Multiple comparisons correction

  #21 opened 5 years ago by arielmadr
  5

• createASVCF.sh with 10X Genomics single cell bams

  #45 opened 3 years ago by adamturner1
  5

• Wrong number of fSNPs using helper scripts

  #51 opened 3 years ago by liesaweigert
  7

• Imputation quality score (IA)

  #50 opened 3 years ago by alperoglu
  0

• Estimated computation time too long

  #48 opened 3 years ago by liesaweigert
  1

• First row of RASQUAL output

  #46 opened 3 years ago by adamturner1
  5

• Expected distribution of Pi

  #49 opened 3 years ago by ccrobertson
  2

• Identical results for close SNP

  #47 opened 3 years ago by Zepeng-Mu
  2

• Estimated computational time is too long ...

  #44 opened 4 years ago by lw157
  4

• QQ plot from rasqual P-values

  #43 opened 4 years ago by plbngl
  17

• MAF filtering with -a uses > rather than >=

  #34 opened 4 years ago by kwcurrin
  1

• QTL Enrichment Analysis

  #42 opened 4 years ago by aileenlikexin
  0

• Permutations and RASQUAL results

  #41 opened 4 years ago by SaideepGona
  1

• ASVCF Memory Usage

  #40 opened 4 years ago by SaideepGona
  6

• Do covariates need to be normalized?

  #38 opened 4 years ago by iamjli
  1

• Mandatory inputs

  #37 opened 4 years ago by js8hh
  3

• Include other covariates

  #39 opened 4 years ago by plbngl
  2

• Visualizing QTLs (coverage boxplot)

  #35 opened 4 years ago by wlwtan
  1

• tutorial for using RASQUAL on ATAC-seq data to find ATAC-QTL

  #36 opened 4 years ago by wlwtan
  1

• 2707 caQTL in RASQUAL paper

  #19 opened 5 years ago by YaCui
  12

• How can reference allele bias be calculated per SNP

  #33 opened 5 years ago by kwcurrin
  6

• Correlated peaks not sharing QTLs

  #32 opened 5 years ago by kwcurrin
  12

• Direction of fragment count and allelic imbalance

  #31 opened 5 years ago by kwcurrin
  6

• Handling peaks with influential points

  #30 opened 5 years ago by kwcurrin
  2

• Number of test SNPs

  #29 opened 5 years ago by raehoonj
  2

• RASQUAL with biological replicates

  #28 opened 5 years ago by agolicz
  3

• Understanding Effect Sizes

  #27 opened 5 years ago by arielmadr
  1

• sample specific offsets

  #26 opened 5 years ago by gouthamatla
  2

• Meta analysis of RASQUAL results from different datasets

  #16 opened 6 years ago by gouthamatla
  3

• Get p-value for each feature-variant test

  #22 opened 5 years ago by liangyy
  7

• Minor allele frequency filtering

  #25 opened 5 years ago by kwcurrin
  3

• Output line without information

  #24 opened 5 years ago by liangyy
  4

• Different output on example run when sample size is increased by 1

  #23 opened 5 years ago by liangyy
  2

• Can we use non sequencing based inputs?

  #20 opened 5 years ago by bioinfograd
  1

• if Indel can be used in VCF input now

  #18 opened 5 years ago by azyro
  3

• "nan" for squared correlation between prior and posterior genotypes (fSNPs)

  #17 opened 5 years ago by gouthamatla
  2

• condition specific eQTLs

  #15 opened 6 years ago by gouthamatla
  2

• Number of fSNPs greater that the specified with -m

  #14 opened 6 years ago by gouthamatla
  2

• Using -m and -l

  #13 opened 6 years ago by gouthamatla
  4

• segmentation fault with covariates file

  #10 opened 6 years ago by girdhar3
  2

• AS counts and permutation test

  #12 opened 6 years ago by gouthamatla
  4