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genesis
•
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0
votes
1
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203
views
GENESIS: error in crossprod
GENESIS
10 weeks ago
Stephanie M. Gogarten
▴ 870
0
votes
2
replies
395
views
GENESIS: Can not use GdsGenotypeReader to read a gds file
GENESIS
GWASTools
GDSfile
updated 4 months ago by
Stephanie M. Gogarten
▴ 870 • written 4 months ago by
Mindy wang
• 0
0
votes
2
replies
389
views
SKAT-O method using GENESIS, question about range iterator using SeqVarWindowIterator
GENESIS
SeqVarTools
updated 5 months ago by
Stephanie M. Gogarten
▴ 870 • written 5 months ago by
pjuge
• 0
1
vote
1
reply
435
views
HOW to FIX - PCAir excludes all my SNPs because there is no chromosome information
GENESIS
autosome-only=FALSE?
PCAir
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
gabry.scata
• 0
0
votes
0
replies
268
views
How many ancestries to send in admixMap() when doing a two-way analysis?
GENESIS
admixMap
6 months ago
mailtoshivam13
• 0
2
votes
5
replies
760
views
assocTestSingle output with GxE
GENESIS
updated 10 months ago by
Stephanie M. Gogarten
▴ 870 • written 10 months ago by
SuperDad
• 0
0
votes
1
reply
433
views
Reference categories for factors
assocTestSingle
GENESIS
written 14 months ago by
SuperD
• 0
0
votes
2
replies
702
views
kinToMatrix creates an empty matrix (except for diagonal 0.5 values)
kingToMatrix
GENESIS
Plants
18 months ago
Monica
• 0
1
vote
2
replies
4.0k
views
Why are my p-values deflated (GWAS)?
gwas
genesis
p-value
q-q-plot
updated 3.2 years ago by
Anna
• 0 • written 4.4 years ago by
solanum
• 0
0
votes
1
reply
827
views
Approximations to Est and Est.SE in GENESIS
GENESIS
3.4 years ago
Stephanie M. Gogarten
▴ 870
0
votes
0
replies
678
views
X chromosome analyses for males in GENESIS
GENESIS
3.5 years ago
Stephanie M. Gogarten
▴ 870
0
votes
3
replies
1.4k
views
Alternate allele for GENESIS?
genesis
effect allele
association analysis
updated 3.7 years ago by
Stephanie M. Gogarten
▴ 870 • written 3.7 years ago by
ucbtapc
• 0
0
votes
1
reply
784
views
using GENESIS R package with non-human species
genesis
gwastools
3.8 years ago
Stephanie M. Gogarten
▴ 870
0
votes
2
replies
899
views
Association testing model in GENESIS
genesis
updated 3.8 years ago by
Stephanie M. Gogarten
▴ 870 • written 3.8 years ago by
o.giannakopoulou
• 0
0
votes
1
reply
1.1k
views
GENESIS multiple gds files
genesis
gds
SeqVarData
updated 3.9 years ago by
Stephanie M. Gogarten
▴ 870 • written 3.9 years ago by
JT
• 0
0
votes
8
replies
1.5k
views
Question: GENESIS: assocTestSingle() is not giving any output; guessing that it is arising from GenotypeBlockIterator()
Genesis
4.2 years ago
alipka
▴ 10
2
votes
1
reply
661
views
Does GENESIS match scan IDs for genotype and phenotype data?
GENESIS
updated 4.2 years ago by
Stephanie M. Gogarten
▴ 870 • written 4.2 years ago by
lassana.a.samarakoon
▴ 10
0
votes
0
replies
859
views
Normalisation of Data before loading in TMixClust
rna-seq
tmixclust
k-means clustering
gene expression
genesis
4.4 years ago
astridite
• 0
2
votes
1
reply
803
views
Why did the Wald test disappear from GENESIS?
genesis
4.5 years ago
Stephanie M. Gogarten
▴ 870
1
vote
3
replies
1.3k
views
Error in fitNullMM from GENESIS package on highly-related samples
GENESIS
4.5 years ago
Corey.Cox
• 0
1
vote
1
reply
989
views
Calculating the z score from wald test association results in GENESIS
GENESIS
zscore
wald
updated 4.5 years ago by
Stephanie M. Gogarten
▴ 870 • written 4.6 years ago by
lassana.a.samarakoon
▴ 10
3
votes
6
replies
1.4k
views
Interpreting the output of score test using GENESIS
genesis
output
score
updated 4.6 years ago by
Stephanie M. Gogarten
▴ 870 • written 4.6 years ago by
lassana.a.samarakoon
▴ 10
2
votes
4
replies
1.1k
views
Sporadic missingness with admixmmap
genesis
admixmap
updated 4.6 years ago by
Stephanie M. Gogarten
▴ 870 • written 4.6 years ago by
GENOMIC_region
• 0
0
votes
3
replies
1.6k
views
Can't install Genesis
Genesis
Installation
updated 4.7 years ago by
Mike Smith
★ 6.5k • written 4.7 years ago by
winstondunnmd
▴ 10
0
votes
3
replies
1.2k
views
GENESIS: ascertainment in GWAS
genesis
fitnullmodel
gwas
ascertainment
updated 4.7 years ago by
mconomos
▴ 70 • written 4.8 years ago by
ferranpauls10
• 0
6
votes
11
replies
2.7k
views
Genesis: doubts with admixMAPMM
genesis
admixmap
updated 5.0 years ago by
Stephanie M. Gogarten
▴ 870 • written 5.0 years ago by
GENOMIC_region
• 0
0
votes
1
reply
910
views
betas for binary outcome
genesis
5.1 years ago
Stephanie M. Gogarten
▴ 870
0
votes
13
replies
2.2k
views
GENESIS pcrelate() write gds file doesn't work
genesis
pcrelate
gds
updated 5.1 years ago by
Stephanie M. Gogarten
▴ 870 • written 5.1 years ago by
o.giannakopoulou
• 0
4
votes
2
replies
1.8k
views
Imputed dosages in GENESIS
genesis
gwastools
seqarray
5.5 years ago • updated 5.2 years ago
Stephanie M. Gogarten
▴ 870
0
votes
1
reply
968
views
Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
GENESIS
GWAS
resampling
resample
statistics
5.2 years ago
naglemi
▴ 10
1
vote
1
reply
924
views
Difference between AssocTestMM (GENESIS) and EMMAX? Why results are different?
GENESIS
GWAS
AssocTestMM
updated 5.4 years ago by
mconomos
▴ 70 • written 5.4 years ago by
naglemi
▴ 10
1
vote
1
reply
906
views
GENESIS pcrelate() to load gds file and continue where the function broke
genesis
pcrrelate
gds
updated 5.5 years ago by
Stephanie M. Gogarten
▴ 870 • written 5.5 years ago by
roll
• 0
0
votes
1
reply
900
views
Using previously calculated PCs in GENESIS
genesis
snprelate
5.6 years ago
Stephanie M. Gogarten
▴ 870
0
votes
1
reply
972
views
Unable to build GDS with more than 255 scaffolds?
GENESIS
GWAS
GDS
updated 5.6 years ago by
zhengx
▴ 30 • written 5.6 years ago by
naglemi
▴ 10
0
votes
1
reply
779
views
selecting SNPs and samples in GENESIS
genesis
5.7 years ago
Stephanie M. Gogarten
▴ 870
0
votes
3
replies
1.2k
views
GENESIS: assocTestMM error for lack of sex chromosome info (not relevant for this species)
GENESIS
assoctestmm
GWAS
updated 5.8 years ago by
mconomos
▴ 70 • written 5.8 years ago by
naglemi
▴ 10
3
votes
4
replies
1.5k
views
Why is assocTestMM running with only a fraction of SNPs in genotype data?
LMM
GWAS
GENESIS
assocTestMM
updated 5.8 years ago by
mconomos
▴ 70 • written 5.8 years ago by
naglemi
▴ 10
2
votes
8
replies
1.7k
views
GENESIS: PCAIR: Error in acc(object, NL[cnode]) : unmatched node provided
genesis
pcair
6.0 years ago
GENOMIC_region
• 0
0
votes
7
replies
1.8k
views
GENESIS: king2mat: subscript out of bounds
genesis
6.0 years ago
Stephanie M. Gogarten
▴ 870
39 results • Page
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Recent ...
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Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Awards
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James W. MacDonald
65k
Supporter
to
JKim
• 0
Popular Question
to
Gordon Smyth
50k
Popular Question
to
Chris
• 0
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to
Jonathan
▴ 10
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Portugal,
1 minute ago
Australia,
5 minutes ago
Wageningen University, Wageningen, the Netherlands,
27 minutes ago
WEHI, Melbourne, Australia,
52 minutes ago
United States,
1 hour ago
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