Showing : GENESIS • reset
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225
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GENESIS: error in crossprod
GENESIS
3 months ago Stephanie M. Gogarten ▴ 870
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2
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426
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GENESIS: Can not use GdsGenotypeReader to read a gds file
GENESIS GWASTools GDSfile
updated 5 months ago by ▴ 870 • written 5 months ago by • 0
0
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2
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415
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SKAT-O method using GENESIS, question about range iterator using SeqVarWindowIterator
GENESIS SeqVarTools
updated 6 months ago by ▴ 870 • written 6 months ago by • 0
1
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1
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467
views
HOW to FIX - PCAir excludes all my SNPs because there is no chromosome information
GENESIS autosome-only=FALSE? PCAir
updated 6 months ago by 65k • written 6 months ago by • 0
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290
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How many ancestries to send in admixMap() when doing a two-way analysis?
GENESIS admixMap
7 months ago mailtoshivam13 • 0
2
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5
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784
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assocTestSingle output with GxE
GENESIS
updated 10 months ago by ▴ 870 • written 10 months ago by • 0
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1
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451
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Reference categories for factors
assocTestSingle GENESIS
written 15 months ago by • 0
0
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2
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715
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kinToMatrix creates an empty matrix (except for diagonal 0.5 values)
kingToMatrix GENESIS Plants
19 months ago • updated 18 months ago Monica • 0
1
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2
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4.1k
views
Why are my p-values deflated (GWAS)?
gwas genesis p-value q-q-plot
updated 3.3 years ago by • 0 • written 4.5 years ago by • 0
0
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1
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852
views
Approximations to Est and Est.SE in GENESIS
GENESIS
3.4 years ago Stephanie M. Gogarten ▴ 870
0
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0
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692
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X chromosome analyses for males in GENESIS
GENESIS
3.5 years ago Stephanie M. Gogarten ▴ 870
0
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3
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1.4k
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Alternate allele for GENESIS?
genesis effect allele association analysis
updated 3.7 years ago by ▴ 870 • written 3.7 years ago by • 0
0
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1
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797
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using GENESIS R package with non-human species
genesis gwastools
3.8 years ago Stephanie M. Gogarten ▴ 870
0
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2
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914
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Association testing model in GENESIS
genesis
updated 3.8 years ago by ▴ 870 • written 3.9 years ago by • 0
0
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1
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1.1k
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GENESIS multiple gds files
genesis gds SeqVarData
updated 3.9 years ago by ▴ 870 • written 3.9 years ago by • 0
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8
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1.5k
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Question: GENESIS: assocTestSingle() is not giving any output; guessing that it is arising from GenotypeBlockIterator()
Genesis
4.3 years ago alipka ▴ 10
2
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1
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674
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Does GENESIS match scan IDs for genotype and phenotype data?
GENESIS
updated 4.3 years ago by ▴ 870 • written 4.3 years ago by ▴ 10
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0
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869
views
Normalisation of Data before loading in TMixClust
rna-seq tmixclust k-means clustering gene expression genesis
4.4 years ago astridite • 0
2
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1
reply
814
views
Why did the Wald test disappear from GENESIS?
genesis
4.5 years ago Stephanie M. Gogarten ▴ 870
1
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3
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1.3k
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Error in fitNullMM from GENESIS package on highly-related samples
GENESIS
4.6 years ago Corey.Cox • 0
1
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1
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1.0k
views
Calculating the z score from wald test association results in GENESIS
GENESIS zscore wald
updated 4.6 years ago by ▴ 870 • written 4.6 years ago by ▴ 10
3
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6
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1.4k
views
Interpreting the output of score test using GENESIS
genesis output score
updated 4.6 years ago by ▴ 870 • written 4.6 years ago by ▴ 10
2
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4
replies
1.1k
views
Sporadic missingness with admixmmap
genesis admixmap
updated 4.7 years ago by ▴ 870 • written 4.7 years ago by • 0
0
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3
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1.7k
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Can't install Genesis
Genesis Installation
updated 4.8 years ago by ★ 6.5k • written 4.8 years ago by ▴ 10
0
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3
replies
1.2k
views
GENESIS: ascertainment in GWAS
genesis fitnullmodel gwas ascertainment
updated 4.8 years ago by ▴ 70 • written 4.8 years ago by • 0
6
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11
replies
2.8k
views
Genesis: doubts with admixMAPMM
genesis admixmap
updated 5.1 years ago by ▴ 870 • written 5.1 years ago by • 0
0
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1
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919
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betas for binary outcome
genesis
5.1 years ago Stephanie M. Gogarten ▴ 870
0
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13
replies
2.3k
views
GENESIS pcrelate() write gds file doesn't work
genesis pcrelate gds
updated 5.2 years ago by ▴ 870 • written 5.2 years ago by • 0
4
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2
replies
1.8k
views
Imputed dosages in GENESIS
genesis gwastools seqarray
5.6 years ago • updated 5.3 years ago Stephanie M. Gogarten ▴ 870
0
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1
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984
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Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
GENESIS GWAS resampling resample statistics
5.3 years ago naglemi ▴ 10
1
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1
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936
views
Difference between AssocTestMM (GENESIS) and EMMAX? Why results are different?
GENESIS GWAS AssocTestMM
updated 5.5 years ago by ▴ 70 • written 5.5 years ago by ▴ 10
1
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1
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927
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GENESIS pcrelate() to load gds file and continue where the function broke
genesis pcrrelate gds
updated 5.5 years ago by ▴ 870 • written 5.5 years ago by • 0
0
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1
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911
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Using previously calculated PCs in GENESIS
genesis snprelate
5.6 years ago Stephanie M. Gogarten ▴ 870
0
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1
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990
views
Unable to build GDS with more than 255 scaffolds?
GENESIS GWAS GDS
updated 5.7 years ago by ▴ 30 • written 5.7 years ago by ▴ 10
0
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1
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791
views
selecting SNPs and samples in GENESIS
genesis
5.8 years ago Stephanie M. Gogarten ▴ 870
0
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3
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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 ▴ 70 • written 5.8 years ago by ▴ 10
3
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4
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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 ▴ 70 • written 5.8 years ago by ▴ 10
2
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8
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1.7k
views
GENESIS: PCAIR: Error in acc(object, NL[cnode]) : unmatched node provided
genesis pcair
6.0 years ago GENOMIC_region • 0
0
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7
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1.8k
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GENESIS: king2mat: subscript out of bounds
genesis
6.0 years ago Stephanie M. Gogarten ▴ 870
39 results • Page 1 of 1
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Comment: Create protein sequences including variants from a VCF file by Yun • 0
This cannot work for a SNV file, since `injectSNPs` need a `SNPlocs` object
Comment: Can log2cpm be used for proteomics data normalization? by Daniel • 0
Thank you for the quick reply and I apologize for it being on the wrong thread but the "post tag" function wasn't working properly.
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
I have arranged the code again following the other post and also the script you suggested. Now, I managed to install `org.Vdahliae.eg.db`. …
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
Thanks again Guido, I will try to run the script you have suggested and see if I can install the package. Yes, I have seen this message a…
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Guido Hooiveld ★ 4.0k
FWIW: based on [previous posts][1] it is suggested to install like this: install.packages(pkgs="./org.Vdahliae.eg.db", repos=NULL, typ…
Votes
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
Answer: SGSeq: moving toward diffex from SGSeq analysis
Answer: How to design DEXSeq formula for multiple variables
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