Showing : GENESIS • reset
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2
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388
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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
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
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2
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700
views
kinToMatrix creates an empty matrix (except for diagonal 0.5 values)
kingToMatrix GENESIS Plants
18 months ago Monica • 0
0
votes
3
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1.2k
views
GENESIS: ascertainment in GWAS
genesis fitnullmodel gwas ascertainment
updated 4.7 years ago by ▴ 70 • written 4.8 years ago by • 0
0
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1
reply
971
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
reply
896
views
Using previously calculated PCs in GENESIS
genesis snprelate
5.6 years ago Stephanie M. Gogarten ▴ 870
1
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1
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904
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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
1
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1
reply
919
views
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
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
0
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1
reply
908
views
betas for binary outcome
genesis
5.1 years ago Stephanie M. Gogarten ▴ 870
6
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11
replies
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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3
replies
1.6k
views
Can't install Genesis
Genesis Installation
updated 4.7 years ago by ★ 6.5k • written 4.7 years ago by ▴ 10
2
votes
4
replies
1.1k
views
Sporadic missingness with admixmmap
genesis admixmap
updated 4.6 years ago by ▴ 870 • written 4.6 years ago by • 0
3
votes
6
replies
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
1
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1
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987
views
Calculating the z score from wald test association results in GENESIS
GENESIS zscore wald
updated 4.5 years ago by ▴ 870 • written 4.6 years ago by ▴ 10
0
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7
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1.8k
views
GENESIS: king2mat: subscript out of bounds
genesis
6.0 years ago Stephanie M. Gogarten ▴ 870
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 ▴ 70 • written 5.8 years ago by ▴ 10
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 5.7 years ago by ▴ 70 • written 5.8 years ago by ▴ 10
0
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1
reply
777
views
selecting SNPs and samples in GENESIS
genesis
5.7 years ago Stephanie M. Gogarten ▴ 870
0
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2
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895
views
Association testing model in GENESIS
genesis
updated 3.8 years ago by ▴ 870 • written 3.8 years ago by • 0
0
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1
reply
781
views
using GENESIS R package with non-human species
genesis gwastools
3.8 years ago Stephanie M. Gogarten ▴ 870
0
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3
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1.4k
views
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
reply
825
views
Approximations to Est and Est.SE in GENESIS
GENESIS
3.4 years ago Stephanie M. Gogarten ▴ 870
0
votes
2
replies
386
views
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
2
votes
5
replies
758
views
assocTestSingle output with GxE
GENESIS
updated 10 months ago by ▴ 870 • written 10 months ago by • 0
1
vote
1
reply
431
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 65k • written 5 months ago by • 0
0
votes
1
reply
200
views
GENESIS: error in crossprod
GENESIS
10 weeks ago Stephanie M. Gogarten ▴ 870
2
votes
1
reply
800
views
Why did the Wald test disappear from GENESIS?
genesis
4.4 years ago Stephanie M. Gogarten ▴ 870
1
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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 • 0 • written 4.4 years ago by • 0
2
votes
1
reply
658
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
0
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1
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1.1k
views
GENESIS multiple gds files
genesis gds SeqVarData
updated 3.9 years ago by ▴ 870 • written 3.9 years ago by • 0
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
0
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1
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965
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
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
0
replies
856
views
Normalisation of Data before loading in TMixClust
rna-seq tmixclust k-means clustering gene expression genesis
4.4 years ago astridite • 0
0
votes
0
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676
views
X chromosome analyses for males in GENESIS
GENESIS
3.4 years ago Stephanie M. Gogarten ▴ 870
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
0
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1
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430
views
Reference categories for factors
assocTestSingle GENESIS
written 14 months ago by • 0
0
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0
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266
views
How many ancestries to send in admixMap() when doing a two-way analysis?
GENESIS admixMap
6 months ago mailtoshivam13 • 0
39 results • Page 1 of 1
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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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