Showing : GENESIS • reset
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281
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Conditional analysis
GENESIS
9 months ago SuperDad • 0
0
votes
1
reply
536
views
GENESIS: error in crossprod
GENESIS
12 months ago Stephanie M. Gogarten ▴ 890
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2
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848
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GENESIS: Can not use GdsGenotypeReader to read a gds file
GENESIS GWASTools GDSfile
updated 14 months ago by ▴ 890 • written 14 months ago by • 0
0
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2
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704
views
SKAT-O method using GENESIS, question about range iterator using SeqVarWindowIterator
GENESIS SeqVarTools
updated 15 months ago by ▴ 890 • written 15 months ago by • 0
1
vote
1
reply
881
views
HOW to FIX - PCAir excludes all my SNPs because there is no chromosome information
GENESIS autosome-only=FALSE? PCAir
updated 15 months ago by 68k • written 15 months ago by ▴ 10
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552
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How many ancestries to send in admixMap() when doing a two-way analysis?
GENESIS admixMap
16 months ago mailtoshivam13 • 0
2
votes
5
replies
1.1k
views
assocTestSingle output with GxE
GENESIS
updated 20 months ago by ▴ 890 • written 20 months ago by • 0
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1
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604
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Reference categories for factors
assocTestSingle GENESIS
written 2.0 years ago by • 0
0
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2
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993
views
kinToMatrix creates an empty matrix (except for diagonal 0.5 values)
kingToMatrix GENESIS Plants
2.3 years ago Monica • 0
1
vote
2
replies
5.0k
views
Why are my p-values deflated (GWAS)?
gwas genesis p-value q-q-plot
updated 4.1 years ago by • 0 • written 5.2 years ago by • 0
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1
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1.1k
views
Approximations to Est and Est.SE in GENESIS
GENESIS
4.2 years ago Stephanie M. Gogarten ▴ 890
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0
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880
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X chromosome analyses for males in GENESIS
GENESIS
4.3 years ago Stephanie M. Gogarten ▴ 890
0
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3
replies
1.8k
views
Alternate allele for GENESIS?
genesis effect allele association analysis
updated 4.5 years ago by ▴ 890 • written 4.5 years ago by • 0
0
votes
1
reply
998
views
using GENESIS R package with non-human species
genesis gwastools
4.6 years ago Stephanie M. Gogarten ▴ 890
0
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2
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1.1k
views
Association testing model in GENESIS
genesis
updated 4.6 years ago by ▴ 890 • written 4.6 years ago by • 0
0
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1
reply
1.5k
views
GENESIS multiple gds files
genesis gds SeqVarData
updated 4.7 years ago by ▴ 890 • written 4.7 years ago by • 0
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8
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1.9k
views
Question: GENESIS: assocTestSingle() is not giving any output; guessing that it is arising from GenotypeBlockIterator()
Genesis
5.0 years ago alipka ▴ 10
2
votes
1
reply
883
views
Does GENESIS match scan IDs for genotype and phenotype data?
GENESIS
updated 5.1 years ago by ▴ 890 • written 5.1 years ago by ▴ 10
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0
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1.1k
views
Normalisation of Data before loading in TMixClust
rna-seq tmixclust k-means clustering gene expression genesis
5.2 years ago astridite • 0
2
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1
reply
1.0k
views
Why did the Wald test disappear from GENESIS?
genesis
5.3 years ago Stephanie M. Gogarten ▴ 890
1
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3
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1.6k
views
Error in fitNullMM from GENESIS package on highly-related samples
GENESIS
5.3 years ago Corey.Cox • 0
1
vote
1
reply
1.2k
views
Calculating the z score from wald test association results in GENESIS
GENESIS zscore wald
updated 5.4 years ago by ▴ 890 • written 5.4 years ago by ▴ 10
3
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6
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1.9k
views
Interpreting the output of score test using GENESIS
genesis output score
updated 5.4 years ago by ▴ 890 • written 5.4 years ago by ▴ 10
2
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4
replies
1.4k
views
Sporadic missingness with admixmmap
genesis admixmap
updated 5.4 years ago by ▴ 890 • written 5.4 years ago by • 0
0
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3
replies
2.2k
views
Can't install Genesis
Genesis Installation
updated 5.5 years ago by ★ 6.6k • written 5.5 years ago by ▴ 10
0
votes
3
replies
1.5k
views
GENESIS: ascertainment in GWAS
genesis fitnullmodel gwas ascertainment
updated 5.6 years ago by ▴ 70 • written 5.6 years ago by • 0
6
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11
replies
3.3k
views
Genesis: doubts with admixMAPMM
genesis admixmap
updated 5.8 years ago by ▴ 890 • written 5.8 years ago by • 0
0
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1
reply
1.1k
views
betas for binary outcome
genesis
5.9 years ago Stephanie M. Gogarten ▴ 890
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13
replies
2.9k
views
GENESIS pcrelate() write gds file doesn't work
genesis pcrelate gds
updated 6.0 years ago by ▴ 890 • written 6.0 years ago by • 0
4
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2
replies
2.1k
views
Imputed dosages in GENESIS
genesis gwastools seqarray
6.4 years ago • updated 6.0 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
6.0 years ago naglemi ▴ 10
1
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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 6.3 years ago by ▴ 70 • written 6.3 years ago by ▴ 10
1
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1
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1.2k
views
GENESIS pcrelate() to load gds file and continue where the function broke
genesis pcrrelate gds
updated 6.3 years ago by ▴ 890 • written 6.3 years ago by • 0
0
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1
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1.1k
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Using previously calculated PCs in GENESIS
genesis snprelate
6.4 years ago Stephanie M. Gogarten ▴ 890
0
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1
reply
1.2k
views
Unable to build GDS with more than 255 scaffolds?
GENESIS GWAS GDS
updated 6.4 years ago by ▴ 30 • written 6.4 years ago by ▴ 10
0
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1
reply
970
views
selecting SNPs and samples in GENESIS
genesis
6.5 years ago Stephanie M. Gogarten ▴ 890
0
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3
replies
1.5k
views
GENESIS: assocTestMM error for lack of sex chromosome info (not relevant for this species)
GENESIS assoctestmm GWAS
updated 6.6 years ago by ▴ 70 • written 6.6 years ago by ▴ 10
3
votes
4
replies
1.8k
views
Why is assocTestMM running with only a fraction of SNPs in genotype data?
LMM GWAS GENESIS assocTestMM
updated 6.6 years ago by ▴ 70 • written 6.6 years ago by ▴ 10
2
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8
replies
2.0k
views
GENESIS: PCAIR: Error in acc(object, NL[cnode]) : unmatched node provided
genesis pcair
6.8 years ago GENOMIC_region • 0
0
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7
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2.2k
views
GENESIS: king2mat: subscript out of bounds
genesis
6.8 years ago Stephanie M. Gogarten ▴ 890
40 results • Page 1 of 1
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Comment: Differential variance analysis - can i use deseq2 by Michael Love 43k
VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…
Answer: Use of limma R package with targeted proteomics for DE analysis by Gordon Smyth 52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
Comment: WGCNA by pammelala304 • 0
Thank you for your time and effort. I am so grateful! Play game [block blast](https://blockblastpuzzle.io) free.
Comment: Does anyone have the command to download all of the core_nt using blast_db_get() by Matthew Thornton ▴ 380
Ok. So I guess the core_nt is over 300Gb compressed. I can do it, but maybe it is better to just use ncbi-tools over the internet and just…
Comment: normalizatino of dna methylation EPIC data by user_bioinfo • 0
yes actually that's why I did, and its all good! thank you for your response
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
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