xihaoli/STAARpipeline-Tutorial

Issues

• What is the difference between the "results_temp" and "results_m" results?

  #68 opened a month ago by jingydz
  1

• Dynamic Window dim(X) error

  #55 opened 5 months ago by GACGAMA
  3

• Error : Mat::operator(): index out of bounds & Error in apply(emthr_SCANG_O, 2, max) :

  #67 opened a month ago by jingydz
  1

• Controls / cases counts inverted when using binary model

  #63 opened 3 months ago by GACGAMA
  7

• Plots for gene centric ncRNA regions

  #60 opened a month ago by samreenzafer
  5

• warning messages in generating the annotated GDS (aGDS) file.

  #62 opened a month ago by jingydz
  3

• in the Step 2: Individual (single-variant) analysis, Error in if (chr == 1) { : argument is of length zero

  #66 opened a month ago by jingydz
  3

• [Suggestion-Implementation] Add information to summary and annotations of results

  #57 opened 5 months ago by GACGAMA
  1

• FATAL ERROR - Too many first alleles as the major allele (~21.5%).

  #61 opened a month ago by jingydz
  1

• variant set in gene-centric coding/noncoding analysis

  #65 opened 2 months ago by eliu98
  2

• Number of jobs

  #31 opened a year ago by pthami07
  4

• kinship matrix

  #64 opened 3 months ago by eliu98
  2

• Ukbiobank Agds files generation

  #59 opened 5 months ago by akhilpampana
  16

• Known_Loci_Pruning error

  #46 opened 5 months ago by jingling000
  2

• Conditional analysis - Summary Gene Centric Noncoding not running to completion

  #58 opened 5 months ago by samreenzafer
  6

• #SNVs per case/control?

  #48 opened 7 months ago by kwdoyle
  1

• Can't annotate individual variant results

  #56 opened 5 months ago by GACGAMA
  2

• STAARpipeline_Gene_Centric_Noncoding

  #54 opened 6 months ago by samreenzafer
  2

• Error in Gene Centric Analysis

  #51 opened 6 months ago by GACGAMA
  1

• Fitting NULL model for binary outcomes

  #50 opened 6 months ago by GACGAMA
  5

• Error in results_plof_genome[, "cMAC"] : subscript out of bounds

  #52 opened 6 months ago by GACGAMA
  2

• Followup Question to Issue #28

  #53 opened 6 months ago by samreenzafer
  2

• fit_nullmodel Output is mostly Null and 0

  #49 opened 6 months ago by samreenzafer
  16

• vcf to gds

  #47 opened 7 months ago by wangshuang2024
  7

• gnomAD AF & family-based vcf analysis

  #34 opened a year ago by XiaKwan
  3

• Error in seqGetData: Invalid dimension 'Start' and 'Length'

  #44 opened 8 months ago by wbs-whuer
  5

• Null outputs from Sliding_Window()

  #45 opened 8 months ago by pelinunal
  2

• Ancestry PCs / kinship

  #39 opened 8 months ago by kwdoyle
  11

• LD_pruning error

  #33 opened 8 months ago by WANGyujian123
  4

• error in running "STAARpipeline_Null_Model.r"

  #43 opened 8 months ago by Jerryliu0024
  7

• Gene Centric Coding Annotation fails

  #41 opened 9 months ago by kwdoyle
  2

• Dynamic_Window_SCANG error(s)

  #40 opened 9 months ago by lj1257111
  3

• Error in fit STAAR null model

  #37 opened 10 months ago by zmli0831
  6

• Error in Fit STAAR null model step: asMethod(object) : matrix is not symmetric [1,2]

  #42 opened 10 months ago by liu-xu-bing
  6

• VCF2GDS

  #35 opened 10 months ago by tytrhr
  5

• Phenofile in STAARpipeline_Null_Model.r

  #32 opened a year ago by SheaCheng2000
  4

• No Manhattan or QQ plots from STAARpipelineSummary_Dynamic_Window.r?

  #38 opened a year ago by kwdoyle
  1

• Gene_Centric_Coding function fails due to character-formatted annotation data

  #36 opened a year ago by kwdoyle
  6

• No known loci for conditional analysis?

  #28 opened a year ago by Dani-kolbe
  1

• Lack of Input Examples for running STAARpipeline

  #30 opened a year ago by cantlap
  1

• Expected input Parameters for Gene Centric Coding Step

  #29 opened a year ago by cantlap
  3

• STAAR sliding window errors

  #26 opened a year ago by Alexei-Lipov
  4

• Running staarpipeline docker image

  #24 opened a year ago by pthami07
  1

• run this pipline in crop population

  #25 opened a year ago by HaoWangLYL
  2

• GENESIS null model not working

  #27 opened a year ago by whtop
  3

• Question about the results of Dynamic_Window_SCANG() and Dynamic_Window_Results_Summary()

  #23 opened 2 years ago by SheaCheng2000
  7

• Small number of variants are passed for analysis

  #20 opened 2 years ago by alohasiqi
  9

• Questions about individual analysis results

  #22 opened 2 years ago by alohasiqi
  2

• "CSV error" when running Annotate.R

  #19 opened 2 years ago by SheaCheng2000
  5

• About rank-based inverse normal transformation

  #21 opened 2 years ago by hmutanqilong
  4