Showing : GENESIS • reset
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Conditional analysis
GENESIS
11 months ago SuperDad • 0
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1
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625
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GENESIS: error in crossprod
GENESIS
14 months ago Stephanie M. Gogarten ▴ 890
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2
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952
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GENESIS: Can not use GdsGenotypeReader to read a gds file
GENESIS GWASTools GDSfile
updated 16 months ago by ▴ 890 • written 16 months ago by • 0
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2
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752
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SKAT-O method using GENESIS, question about range iterator using SeqVarWindowIterator
GENESIS SeqVarTools
updated 17 months ago by ▴ 890 • written 17 months ago by • 0
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1
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955
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HOW to FIX - PCAir excludes all my SNPs because there is no chromosome information
GENESIS autosome-only=FALSE? PCAir
updated 17 months ago by 68k • written 17 months ago by ▴ 10
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594
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How many ancestries to send in admixMap() when doing a two-way analysis?
GENESIS admixMap
18 months ago mailtoshivam13 • 0
2
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5
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1.2k
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assocTestSingle output with GxE
GENESIS
updated 22 months ago by ▴ 890 • written 22 months ago by • 0
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627
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Reference categories for factors
assocTestSingle GENESIS
written 2.2 years ago by • 0
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2
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1.0k
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kinToMatrix creates an empty matrix (except for diagonal 0.5 values)
kingToMatrix GENESIS Plants
2.5 years ago Monica • 0
1
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2
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5.1k
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Why are my p-values deflated (GWAS)?
gwas genesis p-value q-q-plot
updated 4.2 years ago by • 0 • written 5.4 years ago by • 0
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1
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1.1k
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Approximations to Est and Est.SE in GENESIS
GENESIS
4.4 years ago Stephanie M. Gogarten ▴ 890
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906
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X chromosome analyses for males in GENESIS
GENESIS
4.4 years ago Stephanie M. Gogarten ▴ 890
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3
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1.9k
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Alternate allele for GENESIS?
genesis effect allele association analysis
updated 4.7 years ago by ▴ 890 • written 4.7 years ago by • 0
0
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1
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1.0k
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using GENESIS R package with non-human species
genesis gwastools
4.8 years ago Stephanie M. Gogarten ▴ 890
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2
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1.2k
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Association testing model in GENESIS
genesis
updated 4.8 years ago by ▴ 890 • written 4.8 years ago by • 0
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1
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1.6k
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GENESIS multiple gds files
genesis gds SeqVarData
updated 4.9 years ago by ▴ 890 • written 4.9 years ago by • 0
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8
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2.0k
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Question: GENESIS: assocTestSingle() is not giving any output; guessing that it is arising from GenotypeBlockIterator()
Genesis
5.2 years ago alipka ▴ 10
2
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1
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933
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Does GENESIS match scan IDs for genotype and phenotype data?
GENESIS
updated 5.2 years ago by ▴ 890 • written 5.2 years ago by ▴ 10
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0
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1.1k
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Normalisation of Data before loading in TMixClust
rna-seq tmixclust k-means clustering gene expression genesis
5.4 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
5.4 years ago Stephanie M. Gogarten ▴ 890
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3
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1.6k
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Error in fitNullMM from GENESIS package on highly-related samples
GENESIS
5.5 years ago Corey.Cox • 0
1
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1
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1.3k
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Calculating the z score from wald test association results in GENESIS
GENESIS zscore wald
updated 5.5 years ago by ▴ 890 • written 5.6 years ago by ▴ 10
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6
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2.0k
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Interpreting the output of score test using GENESIS
genesis output score
updated 5.6 years ago by ▴ 890 • written 5.6 years ago by ▴ 10
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4
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1.4k
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Sporadic missingness with admixmmap
genesis admixmap
updated 5.6 years ago by ▴ 890 • written 5.6 years ago by • 0
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3
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2.4k
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Can't install Genesis
Genesis Installation
updated 5.7 years ago by ★ 6.6k • written 5.7 years ago by ▴ 10
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3
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1.5k
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GENESIS: ascertainment in GWAS
genesis fitnullmodel gwas ascertainment
updated 5.7 years ago by ▴ 70 • written 5.8 years ago by • 0
6
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11
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3.4k
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Genesis: doubts with admixMAPMM
genesis admixmap
updated 6.0 years ago by ▴ 890 • written 6.0 years ago by • 0
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1
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1.2k
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betas for binary outcome
genesis
6.1 years ago Stephanie M. Gogarten ▴ 890
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13
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3.0k
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GENESIS pcrelate() write gds file doesn't work
genesis pcrelate gds
updated 6.1 years ago by ▴ 890 • written 6.1 years ago by • 0
4
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2
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2.1k
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Imputed dosages in GENESIS
genesis gwastools seqarray
6.5 years ago • updated 6.2 years ago Stephanie M. Gogarten ▴ 890
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1
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1.2k
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Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
GENESIS GWAS resampling resample statistics
6.2 years ago naglemi ▴ 10
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1
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1.2k
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Difference between AssocTestMM (GENESIS) and EMMAX? Why results are different?
GENESIS GWAS AssocTestMM
updated 6.4 years ago by ▴ 70 • written 6.4 years ago by ▴ 10
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1
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1.2k
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GENESIS pcrelate() to load gds file and continue where the function broke
genesis pcrrelate gds
updated 6.5 years ago by ▴ 890 • written 6.5 years ago by • 0
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1
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1.1k
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Using previously calculated PCs in GENESIS
genesis snprelate
6.6 years ago Stephanie M. Gogarten ▴ 890
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1
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1.3k
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Unable to build GDS with more than 255 scaffolds?
GENESIS GWAS GDS
updated 6.6 years ago by ▴ 30 • written 6.6 years ago by ▴ 10
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1
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1.0k
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selecting SNPs and samples in GENESIS
genesis
6.7 years ago Stephanie M. Gogarten ▴ 890
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3
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1.5k
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GENESIS: assocTestMM error for lack of sex chromosome info (not relevant for this species)
GENESIS assoctestmm GWAS
updated 6.7 years ago by ▴ 70 • written 6.8 years ago by ▴ 10
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4
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1.8k
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Why is assocTestMM running with only a fraction of SNPs in genotype data?
LMM GWAS GENESIS assocTestMM
updated 6.8 years ago by ▴ 70 • written 6.8 years ago by ▴ 10
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8
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2.1k
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GENESIS: PCAIR: Error in acc(object, NL[cnode]) : unmatched node provided
genesis pcair
7.0 years ago GENOMIC_region • 0
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7
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2.2k
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GENESIS: king2mat: subscript out of bounds
genesis
7.0 years ago Stephanie M. Gogarten ▴ 890
40 results • Page 1 of 1
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Replies
Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Answer: Analyzing TnSeq data with DESeq2 by cold.wolverine.arku • 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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