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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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LDpruning really using num.threads?
#59
rafalcode
opened
5 years ago
2
error with snpgdsGEN2GDS
#58
gianolga
closed
5 years ago
2
snpgdsIBDSelection fails for large matrices
#57
smgogarten
closed
5 years ago
1
question about snpgdsPCA
#56
xingwu2
closed
5 years ago
0
SNPRelate snpgdsLDMat and snpgdsLDpruning problem
#55
thierrygosselin
closed
5 years ago
2
is.character(vcf.fn) & is.vector(vcf.fn) is not TRUE
#54
PlantDr430
closed
5 years ago
1
remove.monosnp in snpgdsLDpruning() ignoring heterozygotes
#53
AAvalos82
closed
5 years ago
6
LD-threshold >1 ?
#52
kroluk
closed
5 years ago
2
Using SNPRelate Results to prune VCF files
#51
TrinityConn
closed
5 years ago
1
How to merge gds files each from 1 chromosome?
#50
evigorito
opened
5 years ago
1
caught segfault 'memory not mapped' with snpgdsPCA
#49
evigorito
opened
5 years ago
1
details of snpgdsLDpruning required
#48
thierrygosselin
closed
5 years ago
2
snpgdsGDS2PED() sample annotation
#47
AAvalos82
closed
4 years ago
2
Using SNPRelate for bacteria genomes?
#46
sofiany
opened
6 years ago
1
remove.monosnp=TRUE remove all SNPs
#45
timedreamer
opened
6 years ago
0
Error in .OpenConnText(vcf.fn) : could not find function ".OpenConnText"
#44
taniachavarria79
opened
6 years ago
0
snpgdsFs fuction/Issue in returning SNP ids list used in the analysis
#43
elenadehnavi
closed
6 years ago
2
Does snpgdsLDpruning calculate squared correlation coefficient?
#42
wvictor14
closed
6 years ago
1
SNPs disappearing?
#41
blgodwin
closed
6 years ago
1
Filtering and snpgdsLDpruning: filter has no effect
#40
flinz
closed
6 years ago
1
snpgdsIndInb not reporting sample id?
#39
jgx65
closed
6 years ago
1
snpgdsLDpruning
#38
jjpadilla
closed
6 years ago
1
all SNPs falsely labelled as monomorphic
#37
webbchen
opened
6 years ago
3
File format of groups file for Admixture analysis
#36
Tman3
opened
6 years ago
3
Output the LD-pruned GDS from SNPRelate for phylogenetic analysis in SNPyhlo
#35
Tman3
closed
6 years ago
3
Error with snpgdsVCF2GDS
#34
annat22
opened
6 years ago
1
the definition of missing rate
#33
nottwy
closed
6 years ago
3
snpgdsOpen error
#32
nottwy
closed
6 years ago
2
invalid pointer: 0x00007ffd7b1b2bf8
#31
ckr123tw
opened
6 years ago
5
R Error : '...' used in the wrong context
#30
marieBvr
closed
6 years ago
2
Error indexing gdsn created from snpgdsVCF2GDS
#29
dvjim
closed
7 years ago
1
Allow returning *only* SNP ids from SNPRateFreq
#28
kdm9
closed
7 years ago
0
Error compiling package with Intel compiler
#27
CreRecombinase
closed
6 years ago
3
The method you take to calculate PCA, IBD and IBS
#26
nottwy
closed
6 years ago
2
snpgdsSampMissRate
#25
jingjin0322
closed
7 years ago
3
snpgdsSlidingWindow brings up "Error in .CheckFile(gdsobj) : `gdsobj' should be a GDS file."
#24
SebVen
closed
7 years ago
9
snpgdsGDS2BED fails to read GDS file made by seqVCF2GDS
#23
timflutre
closed
7 years ago
2
Description file: Depends and Suggests
#22
thierrygosselin
closed
7 years ago
1
systematic upward bias with `SNPRelate::snpgdsFst`
#21
thierrygosselin
opened
7 years ago
6
SNP ID
#20
elizeng
closed
8 years ago
1
Simulate IBD for known relationships
#19
elizeng
opened
8 years ago
1
Exporting snpgdsCutTree data into a JSON format?
#18
brspurri
closed
8 years ago
2
deadlocks
#17
kforner
opened
8 years ago
0
what method of clustering do you use?
#16
orchid00
closed
8 years ago
2
Arbitrary chromosome numbers
#15
mycecilia
closed
9 years ago
2
error in snpgdsPCACorr with SeqArray file
#14
smgogarten
closed
9 years ago
0
add.gdsn not work correctly
#13
lian0090
closed
9 years ago
4
Update ConvToGDS.cpp
#12
NikNakk
closed
9 years ago
1
error installing from bioconductor
#11
eparejatobes
closed
9 years ago
2
Fails on large vcf
#10
Gibbsdavidl
closed
9 years ago
5
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