Showing : GENESIS • reset
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298
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Conditional analysis
GENESIS
10 months ago SuperDad • 0
0
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1
reply
582
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GENESIS: error in crossprod
GENESIS
13 months ago Stephanie M. Gogarten ▴ 890
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2
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897
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GENESIS: Can not use GdsGenotypeReader to read a gds file
GENESIS GWASTools GDSfile
updated 15 months ago by ▴ 890 • written 15 months ago by • 0
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2
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734
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SKAT-O method using GENESIS, question about range iterator using SeqVarWindowIterator
GENESIS SeqVarTools
updated 16 months ago by ▴ 890 • written 16 months ago by • 0
1
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1
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921
views
HOW to FIX - PCAir excludes all my SNPs because there is no chromosome information
GENESIS autosome-only=FALSE? PCAir
updated 16 months ago by 68k • written 16 months ago by ▴ 10
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575
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How many ancestries to send in admixMap() when doing a two-way analysis?
GENESIS admixMap
17 months ago mailtoshivam13 • 0
2
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5
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1.2k
views
assocTestSingle output with GxE
GENESIS
updated 21 months ago by ▴ 890 • written 21 months ago by • 0
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1
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616
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Reference categories for factors
assocTestSingle GENESIS
written 2.1 years ago by • 0
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2
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1.0k
views
kinToMatrix creates an empty matrix (except for diagonal 0.5 values)
kingToMatrix GENESIS Plants
2.4 years ago Monica • 0
1
vote
2
replies
5.1k
views
Why are my p-values deflated (GWAS)?
gwas genesis p-value q-q-plot
updated 4.1 years ago by • 0 • written 5.3 years ago by • 0
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1
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1.1k
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Approximations to Est and Est.SE in GENESIS
GENESIS
4.3 years ago Stephanie M. Gogarten ▴ 890
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0
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891
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X chromosome analyses for males in GENESIS
GENESIS
4.4 years ago Stephanie M. Gogarten ▴ 890
0
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3
replies
1.9k
views
Alternate allele for GENESIS?
genesis effect allele association analysis
updated 4.6 years ago by ▴ 890 • written 4.6 years ago by • 0
0
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1
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1.0k
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using GENESIS R package with non-human species
genesis gwastools
4.7 years ago Stephanie M. Gogarten ▴ 890
0
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2
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1.2k
views
Association testing model in GENESIS
genesis
updated 4.7 years ago by ▴ 890 • written 4.7 years ago by • 0
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1
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1.5k
views
GENESIS multiple gds files
genesis gds SeqVarData
updated 4.8 years ago by ▴ 890 • written 4.8 years ago by • 0
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8
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2.0k
views
Question: GENESIS: assocTestSingle() is not giving any output; guessing that it is arising from GenotypeBlockIterator()
Genesis
5.1 years ago alipka ▴ 10
2
votes
1
reply
907
views
Does GENESIS match scan IDs for genotype and phenotype data?
GENESIS
updated 5.1 years ago by ▴ 890 • written 5.1 years ago by ▴ 10
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0
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1.1k
views
Normalisation of Data before loading in TMixClust
rna-seq tmixclust k-means clustering gene expression genesis
5.3 years ago astridite • 0
2
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1
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1.0k
views
Why did the Wald test disappear from GENESIS?
genesis
5.4 years ago Stephanie M. Gogarten ▴ 890
1
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3
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1.6k
views
Error in fitNullMM from GENESIS package on highly-related samples
GENESIS
5.4 years ago Corey.Cox • 0
1
vote
1
reply
1.3k
views
Calculating the z score from wald test association results in GENESIS
GENESIS zscore wald
updated 5.4 years ago by ▴ 890 • written 5.5 years ago by ▴ 10
3
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6
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1.9k
views
Interpreting the output of score test using GENESIS
genesis output score
updated 5.5 years ago by ▴ 890 • written 5.5 years ago by ▴ 10
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4
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1.4k
views
Sporadic missingness with admixmmap
genesis admixmap
updated 5.5 years ago by ▴ 890 • written 5.5 years ago by • 0
0
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3
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2.3k
views
Can't install Genesis
Genesis Installation
updated 5.6 years ago by ★ 6.6k • written 5.6 years ago by ▴ 10
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3
replies
1.5k
views
GENESIS: ascertainment in GWAS
genesis fitnullmodel gwas ascertainment
updated 5.6 years ago by ▴ 70 • written 5.7 years ago by • 0
6
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11
replies
3.3k
views
Genesis: doubts with admixMAPMM
genesis admixmap
updated 5.9 years ago by ▴ 890 • written 5.9 years ago by • 0
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1
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1.2k
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betas for binary outcome
genesis
6.0 years ago Stephanie M. Gogarten ▴ 890
0
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13
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2.9k
views
GENESIS pcrelate() write gds file doesn't work
genesis pcrelate gds
updated 6.0 years ago by ▴ 890 • written 6.0 years ago by • 0
4
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2
replies
2.1k
views
Imputed dosages in GENESIS
genesis gwastools seqarray
6.4 years ago • updated 6.1 years ago Stephanie M. Gogarten ▴ 890
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1
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1.2k
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Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
GENESIS GWAS resampling resample statistics
6.1 years ago naglemi ▴ 10
1
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1
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1.2k
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Difference between AssocTestMM (GENESIS) and EMMAX? Why results are different?
GENESIS GWAS AssocTestMM
updated 6.3 years ago by ▴ 70 • written 6.3 years ago by ▴ 10
1
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1
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1.2k
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GENESIS pcrelate() to load gds file and continue where the function broke
genesis pcrrelate gds
updated 6.4 years ago by ▴ 890 • written 6.4 years ago by • 0
0
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1
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1.1k
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Using previously calculated PCs in GENESIS
genesis snprelate
6.5 years ago Stephanie M. Gogarten ▴ 890
0
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1
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1.3k
views
Unable to build GDS with more than 255 scaffolds?
GENESIS GWAS GDS
updated 6.5 years ago by ▴ 30 • written 6.5 years ago by ▴ 10
0
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1
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990
views
selecting SNPs and samples in GENESIS
genesis
6.6 years ago Stephanie M. Gogarten ▴ 890
0
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3
replies
1.5k
views
GENESIS: assocTestMM error for lack of sex chromosome info (not relevant for this species)
GENESIS assoctestmm GWAS
updated 6.6 years ago by ▴ 70 • written 6.7 years ago by ▴ 10
3
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4
replies
1.8k
views
Why is assocTestMM running with only a fraction of SNPs in genotype data?
LMM GWAS GENESIS assocTestMM
updated 6.7 years ago by ▴ 70 • written 6.7 years ago by ▴ 10
2
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8
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2.1k
views
GENESIS: PCAIR: Error in acc(object, NL[cnode]) : unmatched node provided
genesis pcair
6.9 years ago GENOMIC_region • 0
0
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7
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2.2k
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GENESIS: king2mat: subscript out of bounds
genesis
6.9 years ago Stephanie M. Gogarten ▴ 890
40 results • Page 1 of 1
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Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with by Gordon Smyth 52k
I generally recommend `block=individual` for unbalanced designs, to recover information from incomplete blocks. I would only be disuaded fr…
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with by Devin ▴ 10
Thank you, Gordon, for your responses to all of my questions. For analysis A), in the case when a patient has either a missing timepoint or…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thanks Michael. Just out of curiosity, would you also use the same technique for things like clustering analysis or when looking at the abn…
Comment: GAGE kegg.gsets() self-signed certificate error by Lucas • 0
Hello, I ended up solving the issue by using the first strategy: Disable the SSL certificate Verification. I used the following code to …
Comment: Clarification on GOALL / GO2ALLORFs mapping by DavideSant • 0
Thank you for your answer James. I have to disagree though, at the SGD webpage you posted there is no indication that "GO:0045719 - negati…
Votes
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using TPM from tximport of Salmon output for singscore
Comment: Using TPM from tximport of Salmon output for singscore
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