Showing : genesis • reset
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223
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GENESIS: error in crossprod
GENESIS
12 weeks ago Stephanie M. Gogarten ▴ 870
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2
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424
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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
1
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1
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459
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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2
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410
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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
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0
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285
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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
replies
781
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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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447
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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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713
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kinToMatrix creates an empty matrix (except for diagonal 0.5 values)
kingToMatrix GENESIS Plants
18 months ago Monica • 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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691
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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
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
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793
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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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913
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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
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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
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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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673
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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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867
views
Normalisation of Data before loading in TMixClust
rna-seq tmixclust k-means clustering gene expression genesis
4.4 years ago astridite • 0
1
vote
2
replies
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 4.4 years ago by • 0
2
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1
reply
810
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
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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
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3
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1.7k
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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
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 5.0 years ago by ▴ 870 • written 5.0 years ago by • 0
0
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1
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918
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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
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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
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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931
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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921
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
4
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2
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1.8k
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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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910
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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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983
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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788
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
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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
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
2
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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
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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
39 results • Page 1 of 1
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Replies
Comment: Can't post a question containing code? by NATASHA • 0
did you find a solution? I´m having the same problem
Comment: error by NATASHA • 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Comment: How to use spike-in information (sequences from another species) with DESeq2::DE by maria.soler • 0
Hi, I have a question barely related to this topic. Do you use a custom reference genome combining your organism and the one used as a spik…
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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