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STAARpipeline-Tutorial
The tutorial for performing single-/multi-trait association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using FAVORannotator, STAARpipeline and STAARpipelineSummary
GNU General Public License v3.0
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kinship matrix
#64
eliu98
closed
1 day ago
2
Controls / cases counts inverted when using binary model
#63
GACGAMA
opened
2 weeks ago
2
warning messages in generating the annotated GDS (aGDS) file.
#62
jingydz
opened
3 weeks ago
1
FATAL ERROR - Too many first alleles as the major allele (~21.5%).
#61
jingydz
opened
3 weeks ago
1
Plots for gene centric ncRNA regions
#60
samreenzafer
opened
2 months ago
0
Ukbiobank Agds files generation
#59
akhilpampana
closed
1 month ago
16
Conditional analysis - Summary Gene Centric Noncoding not running to completion
#58
samreenzafer
opened
2 months ago
6
[Suggestion-Implementation] Add information to summary and annotations of results
#57
GACGAMA
opened
2 months ago
0
Can't annotate individual variant results
#56
GACGAMA
closed
2 months ago
2
Dynamic Window dim(X) error
#55
GACGAMA
closed
2 months ago
2
STAARpipeline_Gene_Centric_Noncoding
#54
samreenzafer
closed
3 months ago
2
Followup Question to Issue #28
#53
samreenzafer
closed
3 months ago
2
Error in results_plof_genome[, "cMAC"] : subscript out of bounds
#52
GACGAMA
closed
3 months ago
2
Error in Gene Centric Analysis
#51
GACGAMA
closed
3 months ago
1
Fitting NULL model for binary outcomes
#50
GACGAMA
closed
3 months ago
5
fit_nullmodel Output is mostly Null and 0
#49
samreenzafer
closed
3 months ago
16
#SNVs per case/control?
#48
kwdoyle
opened
3 months ago
1
vcf to gds
#47
wangshuang2024
closed
4 months ago
7
Known_Loci_Pruning error
#46
jingling000
closed
1 month ago
2
Null outputs from Sliding_Window()
#45
pelinunal
closed
4 months ago
2
Error in seqGetData: Invalid dimension 'Start' and 'Length'
#44
wbs-whuer
closed
4 months ago
5
error in running "STAARpipeline_Null_Model.r"
#43
Jerryliu0024
closed
4 months ago
7
Error in Fit STAAR null model step: asMethod(object) : matrix is not symmetric [1,2]
#42
liu-xu-bing
closed
7 months ago
6
Gene Centric Coding Annotation fails
#41
kwdoyle
closed
6 months ago
2
Dynamic_Window_SCANG error(s)
#40
lj1257111
closed
6 months ago
3
Ancestry PCs / kinship
#39
kwdoyle
closed
4 months ago
11
No Manhattan or QQ plots from STAARpipelineSummary_Dynamic_Window.r?
#38
kwdoyle
closed
8 months ago
1
Error in fit STAAR null model
#37
zmli0831
closed
7 months ago
6
Gene_Centric_Coding function fails due to character-formatted annotation data
#36
kwdoyle
closed
8 months ago
6
VCF2GDS
#35
tytrhr
closed
7 months ago
5
gnomAD AF & family-based vcf analysis
#34
XiaKwan
opened
8 months ago
3
LD_pruning error
#33
WANGyujian123
closed
4 months ago
4
Phenofile in STAARpipeline_Null_Model.r
#32
SheaCheng2000
closed
7 months ago
4
Number of jobs
#31
pthami07
closed
1 year ago
2
Lack of Input Examples for running STAARpipeline
#30
cantlap
closed
1 year ago
1
Expected input Parameters for Gene Centric Coding Step
#29
cantlap
closed
1 year ago
3
No known loci for conditional analysis?
#28
Dani-kolbe
closed
1 year ago
1
GENESIS null model not working
#27
whtop
closed
1 year ago
3
STAAR sliding window errors
#26
Alexei-Lipov
closed
1 year ago
4
run this pipline in crop population
#25
HaoWangLYL
closed
1 year ago
2
Running staarpipeline docker image
#24
pthami07
closed
1 year ago
1
Question about the results of Dynamic_Window_SCANG() and Dynamic_Window_Results_Summary()
#23
SheaCheng2000
closed
1 year ago
7
Questions about individual analysis results
#22
alohasiqi
closed
1 year ago
2
About rank-based inverse normal transformation
#21
hmutanqilong
closed
1 year ago
4
Small number of variants are passed for analysis
#20
alohasiqi
closed
1 year ago
9
"CSV error" when running Annotate.R
#19
SheaCheng2000
closed
1 year ago
5
RESULT: gene centric coding
#18
DamienTan
closed
1 year ago
5
"Coding mask" AND "Noncoding mask"
#17
DamienTan
closed
1 year ago
5
Step 3.2: Gene-centric noncoding analysis
#16
daniel-hui
closed
1 year ago
9
Error in Gene_Centric_Coding analysis
#15
pelinunal
closed
1 year ago
5
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