Showing : Genesis • reset
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Conditional analysis
GENESIS
18 months ago SuperDad • 0
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1
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776
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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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935
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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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716
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How many ancestries to send in admixMap() when doing a two-way analysis?
GENESIS admixMap
2.1 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 2.4 years ago by ▴ 890 • written 2.5 years ago by • 0
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1
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711
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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
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kinToMatrix creates an empty matrix (except for diagonal 0.5 values)
kingToMatrix GENESIS Plants
3.1 years ago Monica • 0
1
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2
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5.5k
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Why are my p-values deflated (GWAS)?
gwas genesis p-value q-q-plot
updated 4.8 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
replies
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
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2
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1.4k
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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
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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
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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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2.2k
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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
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Sporadic missingness with admixmmap
genesis admixmap
updated 6.2 years ago by ▴ 890 • written 6.2 years ago by • 0
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3
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2.6k
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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
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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
replies
3.7k
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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 6.8 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
6.8 years ago naglemi ▴ 10
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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
7.3 years ago Stephanie M. Gogarten ▴ 890
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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 7.4 years ago by ▴ 70 • written 7.4 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 7.4 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: 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.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
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
Awards • All
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
Popular Question to James W. MacDonald 68k
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