Showing : GENESIS • reset
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GENESIS: error in crossprod
GENESIS
9 weeks ago Stephanie M. Gogarten ▴ 870
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2
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380
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GENESIS: Can not use GdsGenotypeReader to read a gds file
GENESIS GWASTools GDSfile
updated 4 months ago by ▴ 870 • written 4 months ago by • 0
0
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2
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384
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SKAT-O method using GENESIS, question about range iterator using SeqVarWindowIterator
GENESIS SeqVarTools
updated 5 months ago by ▴ 870 • written 5 months ago by • 0
1
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1
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429
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HOW to FIX - PCAir excludes all my SNPs because there is no chromosome information
GENESIS autosome-only=FALSE? PCAir
updated 5 months ago by 65k • written 5 months ago by • 0
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262
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How many ancestries to send in admixMap() when doing a two-way analysis?
GENESIS admixMap
6 months ago mailtoshivam13 • 0
2
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5
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754
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assocTestSingle output with GxE
GENESIS
updated 9 months ago by ▴ 870 • written 10 months ago by • 0
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1
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425
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Reference categories for factors
assocTestSingle GENESIS
written 14 months ago by • 0
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2
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695
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kinToMatrix creates an empty matrix (except for diagonal 0.5 values)
kingToMatrix GENESIS Plants
18 months ago Monica • 0
1
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2
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4.0k
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Why are my p-values deflated (GWAS)?
gwas genesis p-value q-q-plot
updated 3.2 years ago by • 0 • written 4.4 years ago by • 0
0
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1
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822
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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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671
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X chromosome analyses for males in GENESIS
GENESIS
3.4 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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777
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using GENESIS R package with non-human species
genesis gwastools
3.7 years ago Stephanie M. Gogarten ▴ 870
0
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2
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890
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Association testing model in GENESIS
genesis
updated 3.8 years ago by ▴ 870 • written 3.8 years ago by • 0
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1
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1.1k
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GENESIS multiple gds files
genesis gds SeqVarData
updated 3.8 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
4.2 years ago alipka ▴ 10
2
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1
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653
views
Does GENESIS match scan IDs for genotype and phenotype data?
GENESIS
updated 4.2 years ago by ▴ 870 • written 4.2 years ago by ▴ 10
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0
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851
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
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793
views
Why did the Wald test disappear from GENESIS?
genesis
4.4 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
4.5 years ago Corey.Cox • 0
1
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1
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981
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Calculating the z score from wald test association results in GENESIS
GENESIS zscore wald
updated 4.5 years ago by ▴ 870 • written 4.5 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 4.5 years ago by ▴ 870 • written 4.5 years ago by ▴ 10
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4
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1.1k
views
Sporadic missingness with admixmmap
genesis admixmap
updated 4.6 years ago by ▴ 870 • written 4.6 years ago by • 0
0
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3
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1.6k
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Can't install Genesis
Genesis Installation
updated 4.7 years ago by ★ 6.5k • written 4.7 years ago by ▴ 10
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3
replies
1.2k
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GENESIS: ascertainment in GWAS
genesis fitnullmodel gwas ascertainment
updated 4.7 years ago by ▴ 70 • written 4.7 years ago by • 0
6
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11
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2.7k
views
Genesis: doubts with admixMAPMM
genesis admixmap
updated 5.0 years ago by ▴ 870 • written 5.0 years ago by • 0
0
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1
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906
views
betas for binary outcome
genesis
5.1 years ago Stephanie M. Gogarten ▴ 870
0
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13
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2.2k
views
GENESIS pcrelate() write gds file doesn't work
genesis pcrelate gds
updated 5.1 years ago by ▴ 870 • written 5.1 years ago by • 0
4
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2
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1.8k
views
Imputed dosages in GENESIS
genesis gwastools seqarray
5.5 years ago • updated 5.2 years ago Stephanie M. Gogarten ▴ 870
0
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1
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961
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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
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1
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914
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Difference between AssocTestMM (GENESIS) and EMMAX? Why results are different?
GENESIS GWAS AssocTestMM
updated 5.4 years ago by ▴ 70 • written 5.4 years ago by ▴ 10
1
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1
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893
views
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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894
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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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962
views
Unable to build GDS with more than 255 scaffolds?
GENESIS GWAS GDS
updated 5.6 years ago by ▴ 30 • written 5.6 years ago by ▴ 10
0
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1
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772
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selecting SNPs and samples in GENESIS
genesis
5.7 years ago Stephanie M. Gogarten ▴ 870
0
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3
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1.2k
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GENESIS: assocTestMM error for lack of sex chromosome info (not relevant for this species)
GENESIS assoctestmm GWAS
updated 5.7 years ago by ▴ 70 • written 5.7 years ago by ▴ 10
3
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4
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1.5k
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Why is assocTestMM running with only a fraction of SNPs in genotype data?
LMM GWAS GENESIS assocTestMM
updated 5.7 years ago by ▴ 70 • written 5.7 years ago by ▴ 10
2
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8
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1.6k
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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: DESeq filtering specific to contrasts by Michael Love 41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0` by isaac.vock • 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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