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SNPRelate
R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)
http://www.bioconductor.org/packages/SNPRelate
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doc: Update snpgdsFst.Rd
#109
Billsfriend
closed
2 weeks ago
0
Error in .InitFile2
#108
Tom159357
opened
4 months ago
1
Error: There is no SNP!
#107
jane-edgeloe
opened
6 months ago
0
agglomerative method in snpgdsHCluster
#106
botanicpanic1
opened
8 months ago
0
Function for matrix-vector multiplication
#105
JianqiaoWang
opened
10 months ago
0
SNP weights
#104
Tannervanorden
opened
10 months ago
0
Adding a new GDS node to my existing GDS file
#103
GabryS3
opened
10 months ago
0
snpgdsLDpruning gives an empty snp dataset
#102
GabryS3
opened
11 months ago
4
Exporting genotype matrix with snp.allele ids instead of 0,1,2 genotype codes from gds file
#101
jpfontenelle
closed
1 year ago
2
Error during installation 3.13.2023
#100
bechee
opened
1 year ago
0
A suggestion
#99
Glaucidium
opened
1 year ago
1
Trouble converting GDS2BED
#98
clorenzo1
opened
1 year ago
0
Combining files
#97
cap76
closed
1 year ago
1
Error when converting vcf to gds
#96
AmanahLW
opened
2 years ago
2
Error in snpgdsVCF2GDS......Genotype code is out of range
#95
gaochengPRC
opened
2 years ago
0
SNPRelate does not check out on current R-Devel
#94
green-striped-gecko
closed
2 years ago
3
SNPRelate for organelle genome (mitochondria or chloroplast)
#93
ucabuk
opened
2 years ago
2
transfer bed into gds
#92
yywyaoyaowu
closed
2 years ago
1
Working with genome that has more than 23 chromosomes?
#91
hsiaoyihung
closed
2 years ago
2
snpgdsLDpruning for getting the number of independent markers for GWAS
#90
MuBulut
opened
2 years ago
2
Sorry, this is a question...
#89
CholoTook
closed
2 years ago
1
Update SNPRelate.Rmd
#88
CholoTook
closed
2 years ago
0
Labeling on HapMap Phase II
#87
Asrix
closed
3 years ago
2
PC-AIR issue when over 50k samples.
#86
jjfarrell
opened
3 years ago
11
Combining GDS files
#85
bio-bench
opened
3 years ago
0
snprelate genotype coding
#84
meixilin
closed
3 years ago
0
Questions around snpgdsPCASNPLoading and snpgdsPCASampLoading
#83
sstadick
closed
3 years ago
2
LAPACK::DSPEVX Error 4
#82
whitejaa
closed
3 years ago
2
Method of handling missing data in snpgdsPCA
#81
andemexoax
closed
3 years ago
2
Population Assignments for PCA plots
#80
carlahurt
opened
3 years ago
1
typo fix: exacting -> extracting
#79
kdm9
closed
3 years ago
0
SNPRelate for parasite genome analysis
#78
vappiah
opened
3 years ago
1
snpgdsCombineGeno makes new snp.id when combine multiple gds files
#77
yangli-ai
opened
3 years ago
2
SNPRelate cannot find variant.id from SeqArray object
#76
yangli-ai
opened
3 years ago
2
How can I modify the y axis (individual dissimilarity)
#75
Carol-Symbiomics
opened
3 years ago
0
I was using vcfMissingness.pl to generate pairwise missingness matrices but after the process went through it says "Fatal error: cannot open file 'resources/missingnessHeatMaps.R': No such file or directory" even if the directory is there. Any input will be appreciated.
#74
mergi-2674
opened
3 years ago
0
snpgdsVCF2GDS not recognizing contigs
#73
cinnamon259
closed
3 years ago
2
Weighted Fst meaning
#72
NamLQ
opened
4 years ago
0
snpgdsIBS: calculation method?
#71
kroluk
closed
4 years ago
4
family information in snpgdsGDS2PED
#70
treebreeder
opened
4 years ago
2
snpgdsLDpruning result to gds/vcf
#69
linsson
opened
4 years ago
7
snpgdsSlidingWindow winstart= bug
#68
marqueda
opened
4 years ago
3
varprop interpretation
#67
MaVdb
closed
4 years ago
7
snpgdsLDpruning gives different number of filtered variants every time.
#66
VenithaB
closed
4 years ago
1
traceXTX is NaN for fastPCA
#65
mchughc
closed
4 years ago
3
PCA with different symbols (pch)
#64
mullerbsf
closed
4 years ago
2
Ids in plink bed are not unique
#63
zillurbmb51
opened
5 years ago
2
offset for grm in snpgdsGRM(method="IndivBeta")
#62
jgx65
closed
5 years ago
4
killed 9 genomat <- snpgdsGetGeno(genofile, sample.id=NULL,snp.id=NULL) Genotype matrix: 10536236 SNPs X 2504 samples Killed: 9
#61
xinghuq
closed
5 years ago
1
Samples names for IBS results
#60
NandiniBN
closed
5 years ago
1
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