Showing : genesis • reset
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Conditional analysis
GENESIS
19 months ago SuperDad • 0
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1
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784
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GENESIS: error in crossprod
GENESIS
22 months ago Stephanie M. Gogarten ▴ 890
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2
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1.2k
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GENESIS: Can not use GdsGenotypeReader to read a gds file
GENESIS GWASTools GDSfile
updated 2.0 years ago by ▴ 890 • written 2.0 years ago by • 0
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2
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946
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SKAT-O method using GENESIS, question about range iterator using SeqVarWindowIterator
GENESIS SeqVarTools
updated 2.1 years ago by ▴ 890 • written 2.1 years ago by • 0
1
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1
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1.2k
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HOW to FIX - PCAir excludes all my SNPs because there is no chromosome information
GENESIS autosome-only=FALSE? PCAir
updated 2.1 years ago by 68k • written 2.1 years ago by ▴ 10
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722
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How many ancestries to send in admixMap() when doing a two-way analysis?
GENESIS admixMap
2.2 years ago mailtoshivam13 • 0
2
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5
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1.5k
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assocTestSingle output with GxE
GENESIS
updated 2.5 years ago by ▴ 890 • written 2.5 years ago by • 0
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1
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716
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Reference categories for factors
assocTestSingle GENESIS
written 2.8 years ago by • 0
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2
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1.3k
views
kinToMatrix creates an empty matrix (except for diagonal 0.5 values)
kingToMatrix GENESIS Plants
3.2 years ago • updated 3.1 years ago Monica • 0
1
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2
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5.6k
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Why are my p-values deflated (GWAS)?
gwas genesis p-value q-q-plot
updated 4.9 years ago by • 0 • written 6.0 years ago by • 0
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1
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1.3k
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Approximations to Est and Est.SE in GENESIS
GENESIS
5.0 years ago Stephanie M. Gogarten ▴ 890
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0
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1.1k
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X chromosome analyses for males in GENESIS
GENESIS
5.1 years ago Stephanie M. Gogarten ▴ 890
0
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3
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2.2k
views
Alternate allele for GENESIS?
genesis effect allele association analysis
updated 5.3 years ago by ▴ 890 • written 5.3 years ago by • 0
0
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1
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1.2k
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using GENESIS R package with non-human species
genesis gwastools
5.4 years ago Stephanie M. Gogarten ▴ 890
0
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2
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1.5k
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Association testing model in GENESIS
genesis
updated 5.4 years ago by ▴ 890 • written 5.4 years ago by • 0
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1
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1.8k
views
GENESIS multiple gds files
genesis gds SeqVarData
updated 5.5 years ago by ▴ 890 • written 5.5 years ago by • 0
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8
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2.4k
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Question: GENESIS: assocTestSingle() is not giving any output; guessing that it is arising from GenotypeBlockIterator()
Genesis
5.8 years ago alipka ▴ 10
2
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1
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1.1k
views
Does GENESIS match scan IDs for genotype and phenotype data?
GENESIS
updated 5.9 years ago by ▴ 890 • written 5.9 years ago by ▴ 10
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0
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1.2k
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Normalisation of Data before loading in TMixClust
rna-seq tmixclust k-means clustering gene expression genesis
6.0 years ago astridite • 0
2
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1
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1.2k
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Why did the Wald test disappear from GENESIS?
genesis
6.1 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
6.1 years ago Corey.Cox • 0
1
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1
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1.4k
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Calculating the z score from wald test association results in GENESIS
GENESIS zscore wald
updated 6.2 years ago by ▴ 890 • written 6.2 years ago by ▴ 10
3
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6
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2.3k
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Interpreting the output of score test using GENESIS
genesis output score
updated 6.2 years ago by ▴ 890 • written 6.2 years ago by ▴ 10
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4
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1.6k
views
Sporadic missingness with admixmmap
genesis admixmap
updated 6.3 years ago by ▴ 890 • written 6.3 years ago by • 0
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3
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2.7k
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Can't install Genesis
Genesis Installation
updated 6.3 years ago by ★ 6.6k • written 6.3 years ago by ▴ 10
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3
replies
1.7k
views
GENESIS: ascertainment in GWAS
genesis fitnullmodel gwas ascertainment
updated 6.4 years ago by ▴ 70 • written 6.4 years ago by • 0
6
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11
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3.7k
views
Genesis: doubts with admixMAPMM
genesis admixmap
updated 6.6 years ago by ▴ 890 • written 6.6 years ago by • 0
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1
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1.3k
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betas for binary outcome
genesis
6.7 years ago Stephanie M. Gogarten ▴ 890
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13
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3.4k
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GENESIS pcrelate() write gds file doesn't work
genesis pcrelate gds
updated 6.8 years ago by ▴ 890 • written 6.8 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
7.2 years ago • updated 6.9 years ago Stephanie M. Gogarten ▴ 890
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1
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1.4k
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Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
GENESIS GWAS resampling resample statistics
6.9 years ago naglemi ▴ 10
1
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1
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1.4k
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Difference between AssocTestMM (GENESIS) and EMMAX? Why results are different?
GENESIS GWAS AssocTestMM
updated 7.1 years ago by ▴ 70 • written 7.1 years ago by ▴ 10
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1
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1.4k
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GENESIS pcrelate() to load gds file and continue where the function broke
genesis pcrrelate gds
updated 7.1 years ago by ▴ 890 • written 7.1 years ago by • 0
0
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1
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1.3k
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Using previously calculated PCs in GENESIS
genesis snprelate
7.2 years ago Stephanie M. Gogarten ▴ 890
0
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1
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1.5k
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Unable to build GDS with more than 255 scaffolds?
GENESIS GWAS GDS
updated 7.2 years ago by ▴ 30 • written 7.2 years ago by ▴ 10
0
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1
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1.1k
views
selecting SNPs and samples in GENESIS
genesis
7.4 years ago Stephanie M. Gogarten ▴ 890
0
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3
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1.7k
views
GENESIS: assocTestMM error for lack of sex chromosome info (not relevant for this species)
GENESIS assoctestmm GWAS
updated 7.4 years ago by ▴ 70 • written 7.4 years ago by ▴ 10
3
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4
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2.1k
views
Why is assocTestMM running with only a fraction of SNPs in genotype data?
LMM GWAS GENESIS assocTestMM
updated 7.4 years ago by ▴ 70 • written 7.4 years ago by ▴ 10
2
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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
7.6 years ago GENOMIC_region • 0
0
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7
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2.6k
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GENESIS: king2mat: subscript out of bounds
genesis
7.6 years ago Stephanie M. Gogarten ▴ 890
40 results • Page 1 of 1
Recent ...
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Comment: Bioinformatician at the Lausanne University Hospital by eja.ger.m • 0
For individuals looking to improve communication and collaboration in demanding medical or research environments like the Genetic Medicine …
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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