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genesis
•
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0
votes
1
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159
views
GENESIS: error in crossprod
GENESIS
6 weeks ago
Stephanie M. Gogarten
▴ 870
0
votes
2
replies
339
views
GENESIS: Can not use GdsGenotypeReader to read a gds file
GENESIS
GWASTools
GDSfile
updated 3 months ago by
Stephanie M. Gogarten
▴ 870 • written 3 months ago by
Mindy wang
• 0
0
votes
2
replies
355
views
SKAT-O method using GENESIS, question about range iterator using SeqVarWindowIterator
GENESIS
SeqVarTools
updated 4 months ago by
Stephanie M. Gogarten
▴ 870 • written 4 months ago by
pjuge
• 0
1
vote
1
reply
402
views
HOW to FIX - PCAir excludes all my SNPs because there is no chromosome information
GENESIS
autosome-only=FALSE?
PCAir
updated 4 months ago by
James W. MacDonald
65k • written 4 months ago by
gabry.scata
• 0
0
votes
0
replies
243
views
How many ancestries to send in admixMap() when doing a two-way analysis?
GENESIS
admixMap
5 months ago
mailtoshivam13
• 0
2
votes
5
replies
725
views
assocTestSingle output with GxE
GENESIS
updated 9 months ago by
Stephanie M. Gogarten
▴ 870 • written 9 months ago by
SuperDad
• 0
0
votes
1
reply
397
views
Reference categories for factors
assocTestSingle
GENESIS
written 13 months ago by
SuperD
• 0
0
votes
2
replies
668
views
kinToMatrix creates an empty matrix (except for diagonal 0.5 values)
kingToMatrix
GENESIS
Plants
17 months ago
Monica
• 0
1
vote
2
replies
3.9k
views
Why are my p-values deflated (GWAS)?
gwas
genesis
p-value
q-q-plot
updated 3.2 years ago by
Anna
• 0 • written 4.3 years ago by
solanum
• 0
0
votes
1
reply
802
views
Approximations to Est and Est.SE in GENESIS
GENESIS
3.3 years ago
Stephanie M. Gogarten
▴ 870
0
votes
0
replies
647
views
X chromosome analyses for males in GENESIS
GENESIS
3.4 years ago
Stephanie M. Gogarten
▴ 870
0
votes
3
replies
1.3k
views
Alternate allele for GENESIS?
genesis
effect allele
association analysis
updated 3.6 years ago by
Stephanie M. Gogarten
▴ 870 • written 3.6 years ago by
ucbtapc
• 0
0
votes
1
reply
762
views
using GENESIS R package with non-human species
genesis
gwastools
3.7 years ago
Stephanie M. Gogarten
▴ 870
0
votes
2
replies
869
views
Association testing model in GENESIS
genesis
updated 3.7 years ago by
Stephanie M. Gogarten
▴ 870 • written 3.7 years ago by
o.giannakopoulou
• 0
0
votes
1
reply
1.1k
views
GENESIS multiple gds files
genesis
gds
SeqVarData
updated 3.8 years ago by
Stephanie M. Gogarten
▴ 870 • written 3.8 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
4.1 years ago
alipka
▴ 10
2
votes
1
reply
633
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
830
views
Normalisation of Data before loading in TMixClust
rna-seq
tmixclust
k-means clustering
gene expression
genesis
4.3 years ago
astridite
• 0
2
votes
1
reply
782
views
Why did the Wald test disappear from GENESIS?
genesis
4.4 years ago
Stephanie M. Gogarten
▴ 870
1
vote
3
replies
1.3k
views
Error in fitNullMM from GENESIS package on highly-related samples
GENESIS
4.4 years ago
Corey.Cox
• 0
1
vote
1
reply
959
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 4.5 years ago by
lassana.a.samarakoon
▴ 10
3
votes
6
replies
1.3k
views
Interpreting the output of score test using GENESIS
genesis
output
score
updated 4.5 years ago by
Stephanie M. Gogarten
▴ 870 • written 4.5 years ago by
lassana.a.samarakoon
▴ 10
2
votes
4
replies
1.0k
views
Sporadic missingness with admixmmap
genesis
admixmap
updated 4.5 years ago by
Stephanie M. Gogarten
▴ 870 • written 4.5 years ago by
GENOMIC_region
• 0
0
votes
3
replies
1.6k
views
Can't install Genesis
Genesis
Installation
updated 4.6 years ago by
Mike Smith
★ 6.5k • written 4.6 years ago by
winstondunnmd
▴ 10
0
votes
3
replies
1.1k
views
GENESIS: ascertainment in GWAS
genesis
fitnullmodel
gwas
ascertainment
updated 4.7 years ago by
mconomos
▴ 70 • written 4.7 years ago by
ferranpauls10
• 0
6
votes
11
replies
2.7k
views
Genesis: doubts with admixMAPMM
genesis
admixmap
updated 4.9 years ago by
Stephanie M. Gogarten
▴ 870 • written 4.9 years ago by
GENOMIC_region
• 0
0
votes
1
reply
875
views
betas for binary outcome
genesis
5.0 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
1.7k
views
Imputed dosages in GENESIS
genesis
gwastools
seqarray
5.5 years ago • updated 5.1 years ago
Stephanie M. Gogarten
▴ 870
0
votes
1
reply
930
views
Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
GENESIS
GWAS
resampling
resample
statistics
5.1 years ago
naglemi
▴ 10
1
vote
1
reply
904
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
877
views
GENESIS pcrelate() to load gds file and continue where the function broke
genesis
pcrrelate
gds
updated 5.4 years ago by
Stephanie M. Gogarten
▴ 870 • written 5.4 years ago by
roll
• 0
0
votes
1
reply
874
views
Using previously calculated PCs in GENESIS
genesis
snprelate
5.5 years ago
Stephanie M. Gogarten
▴ 870
0
votes
1
reply
941
views
Unable to build GDS with more than 255 scaffolds?
GENESIS
GWAS
GDS
updated 5.5 years ago by
zhengx
▴ 30 • written 5.5 years ago by
naglemi
▴ 10
0
votes
1
reply
753
views
selecting SNPs and samples in GENESIS
genesis
5.6 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 5.7 years ago by
mconomos
▴ 70 • written 5.7 years ago by
naglemi
▴ 10
3
votes
4
replies
1.4k
views
Why is assocTestMM running with only a fraction of SNPs in genotype data?
LMM
GWAS
GENESIS
assocTestMM
updated 5.7 years ago by
mconomos
▴ 70 • written 5.7 years ago by
naglemi
▴ 10
2
votes
8
replies
1.6k
views
GENESIS: PCAIR: Error in acc(object, NL[cnode]) : unmatched node provided
genesis
pcair
5.9 years ago
GENOMIC_region
• 0
0
votes
7
replies
1.7k
views
GENESIS: king2mat: subscript out of bounds
genesis
5.9 years ago
Stephanie M. Gogarten
▴ 870
39 results • Page
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Recent ...
Replies
Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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