Showing : genesis • reset
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Conditional analysis
GENESIS
16 months ago SuperDad • 0
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1
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731
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GENESIS: error in crossprod
GENESIS
20 months ago Stephanie M. Gogarten ▴ 890
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2
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1.1k
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GENESIS: Can not use GdsGenotypeReader to read a gds file
GENESIS GWASTools GDSfile
updated 22 months ago by ▴ 890 • written 22 months ago by • 0
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2
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879
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SKAT-O method using GENESIS, question about range iterator using SeqVarWindowIterator
GENESIS SeqVarTools
updated 23 months ago by ▴ 890 • written 23 months ago by • 0
1
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1
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1.1k
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HOW to FIX - PCAir excludes all my SNPs because there is no chromosome information
GENESIS autosome-only=FALSE? PCAir
updated 23 months ago by 68k • written 23 months ago by ▴ 10
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673
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How many ancestries to send in admixMap() when doing a two-way analysis?
GENESIS admixMap
24 months ago mailtoshivam13 • 0
2
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5
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1.4k
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assocTestSingle output with GxE
GENESIS
updated 2.3 years ago by ▴ 890 • written 2.3 years ago by • 0
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1
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684
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Reference categories for factors
assocTestSingle GENESIS
written 2.7 years ago by • 0
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2
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1.2k
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kinToMatrix creates an empty matrix (except for diagonal 0.5 values)
kingToMatrix GENESIS Plants
3.0 years ago Monica • 0
1
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2
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5.4k
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Why are my p-values deflated (GWAS)?
gwas genesis p-value q-q-plot
updated 4.7 years ago by • 0 • written 5.9 years ago by • 0
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1
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1.2k
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Approximations to Est and Est.SE in GENESIS
GENESIS
4.8 years ago Stephanie M. Gogarten ▴ 890
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0
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1.0k
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X chromosome analyses for males in GENESIS
GENESIS
4.9 years ago Stephanie M. Gogarten ▴ 890
0
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3
replies
2.1k
views
Alternate allele for GENESIS?
genesis effect allele association analysis
updated 5.1 years ago by ▴ 890 • written 5.1 years ago by • 0
0
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1
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1.1k
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using GENESIS R package with non-human species
genesis gwastools
5.2 years ago Stephanie M. Gogarten ▴ 890
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2
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1.4k
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Association testing model in GENESIS
genesis
updated 5.3 years ago by ▴ 890 • written 5.3 years ago by • 0
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1
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1.7k
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GENESIS multiple gds files
genesis gds SeqVarData
updated 5.3 years ago by ▴ 890 • written 5.3 years ago by • 0
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8
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2.3k
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Question: GENESIS: assocTestSingle() is not giving any output; guessing that it is arising from GenotypeBlockIterator()
Genesis
5.7 years ago alipka ▴ 10
2
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1
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1.0k
views
Does GENESIS match scan IDs for genotype and phenotype data?
GENESIS
updated 5.7 years ago by ▴ 890 • written 5.7 years ago by ▴ 10
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0
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1.2k
views
Normalisation of Data before loading in TMixClust
rna-seq tmixclust k-means clustering gene expression genesis
5.8 years ago astridite • 0
2
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1
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1.1k
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Why did the Wald test disappear from GENESIS?
genesis
5.9 years ago Stephanie M. Gogarten ▴ 890
1
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3
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1.8k
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Error in fitNullMM from GENESIS package on highly-related samples
GENESIS
6.0 years ago Corey.Cox • 0
1
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1
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1.4k
views
Calculating the z score from wald test association results in GENESIS
GENESIS zscore wald
updated 6.0 years ago by ▴ 890 • written 6.0 years ago by ▴ 10
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6
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2.2k
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Interpreting the output of score test using GENESIS
genesis output score
updated 6.0 years ago by ▴ 890 • written 6.0 years ago by ▴ 10
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4
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1.5k
views
Sporadic missingness with admixmmap
genesis admixmap
updated 6.1 years ago by ▴ 890 • written 6.1 years ago by • 0
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3
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2.6k
views
Can't install Genesis
Genesis Installation
updated 6.2 years ago by ★ 6.6k • written 6.2 years ago by ▴ 10
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3
replies
1.7k
views
GENESIS: ascertainment in GWAS
genesis fitnullmodel gwas ascertainment
updated 6.2 years ago by ▴ 70 • written 6.2 years ago by • 0
6
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11
replies
3.6k
views
Genesis: doubts with admixMAPMM
genesis admixmap
updated 6.5 years ago by ▴ 890 • written 6.5 years ago by • 0
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1
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1.3k
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betas for binary outcome
genesis
6.5 years ago Stephanie M. Gogarten ▴ 890
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13
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3.3k
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GENESIS pcrelate() write gds file doesn't work
genesis pcrelate gds
updated 6.6 years ago by ▴ 890 • written 6.6 years ago by • 0
4
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2
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2.3k
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Imputed dosages in GENESIS
genesis gwastools seqarray
7.0 years ago • updated 6.7 years ago Stephanie M. Gogarten ▴ 890
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1
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1.3k
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Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
GENESIS GWAS resampling resample statistics
6.7 years ago naglemi ▴ 10
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1
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1.4k
views
Difference between AssocTestMM (GENESIS) and EMMAX? Why results are different?
GENESIS GWAS AssocTestMM
updated 6.9 years ago by ▴ 70 • written 6.9 years ago by ▴ 10
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1
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1.3k
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GENESIS pcrelate() to load gds file and continue where the function broke
genesis pcrrelate gds
updated 6.9 years ago by ▴ 890 • written 6.9 years ago by • 0
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1
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1.2k
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Using previously calculated PCs in GENESIS
genesis snprelate
7.0 years ago Stephanie M. Gogarten ▴ 890
0
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1
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1.4k
views
Unable to build GDS with more than 255 scaffolds?
GENESIS GWAS GDS
updated 7.1 years ago by ▴ 30 • written 7.1 years ago by ▴ 10
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1
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1.1k
views
selecting SNPs and samples in GENESIS
genesis
7.2 years ago Stephanie M. Gogarten ▴ 890
0
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3
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1.7k
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GENESIS: assocTestMM error for lack of sex chromosome info (not relevant for this species)
GENESIS assoctestmm GWAS
updated 7.2 years ago by ▴ 70 • written 7.2 years ago by ▴ 10
3
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4
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2.0k
views
Why is assocTestMM running with only a fraction of SNPs in genotype data?
LMM GWAS GENESIS assocTestMM
updated 7.2 years ago by ▴ 70 • written 7.2 years ago by ▴ 10
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8
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2.3k
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GENESIS: PCAIR: Error in acc(object, NL[cnode]) : unmatched node provided
genesis pcair
7.4 years ago GENOMIC_region • 0
0
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7
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2.4k
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GENESIS: king2mat: subscript out of bounds
genesis
7.4 years ago Stephanie M. Gogarten ▴ 890
40 results • Page 1 of 1
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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