Showing : GWASTools • reset
1
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GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and workflow
GWASTools qualitycontrol HumanOmni5-4BeadChip GenomeStudio illumina
updated 8.0 years ago by ▴ 870 • written 8.0 years ago by • 0
0
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3
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2.6k
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Affymetrix CEL files
cdf GWASTools cdf GWASTools
updated 11.1 years ago by 65k • written 11.1 years ago by ▴ 870
0
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1
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2.5k
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help with analysis of genotyping data from Illumina HumanOmni5-4v1_B chip
SNP VariantAnnotation Annotation probe VariantAnnotation GWASTools SNP VariantAnnotation
updated 10.0 years ago by ▴ 870 • written 10.0 years ago by ▴ 160
0
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6
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2.2k
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Error using readVcf
gwastools variantannotation
updated 6.9 years ago by ▴ 870 • written 6.9 years ago by • 0
0
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1
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2.2k
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GWASTools
cdf GWASTools cdf GWASTools
10.8 years ago Stephanie M. Gogarten ▴ 870
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0
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1.9k
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GWASTools
Organism GWASTools Organism GWASTools SNPRelate
11.2 years ago Stephanie M. Gogarten ▴ 870
0
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4
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1.9k
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how to save subsetted GDS file
gwastools
written 6.0 years ago by ▴ 30
0
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0
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1.8k
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snpStats/GWASTools conversion
cdf convert snpMatrix snpStats GWASTools cdf convert snpMatrix snpStats GWASTools
10.6 years ago Stephanie M. Gogarten ▴ 870
0
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2
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1.8k
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Creating Intensity GDS file for the R package GWAStools
gwastools idat gds format
updated 6.8 years ago by ▴ 870 • written 6.8 years ago by • 0
2
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1
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1.8k
views
PLINK features available in GWASTools?
gwastools
9.0 years ago Stephanie M. Gogarten ▴ 870
1
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5
replies
1.8k
views
"set genotype" function for gds?
gwastools gds
7.3 years ago Lna • 0
4
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2
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1.8k
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Imputed dosages in GENESIS
genesis gwastools seqarray
5.6 years ago • updated 5.3 years ago Stephanie M. Gogarten ▴ 870
0
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2
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1.8k
views
Permutations of GWAS for GWASTools
gwastools
updated 8.7 years ago by ▴ 870 • written 8.7 years ago by • 0
3
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2
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1.8k
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Minimum allele frequency (MAF) from a Genomic Data Structure (GDS) file
snprelate GWASTools
updated 8.0 years ago by ▴ 30 • written 8.0 years ago by ▴ 40
0
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5
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1.8k
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GWATools use in creating ncdf files
SNP Annotation cdf GWASTools SNP Annotation cdf GWASTools
updated 11.0 years ago by ▴ 60 • written 11.0 years ago by ▴ 870
2
votes
1
reply
1.7k
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Meaning of NA for LRR and BAF values estimated with GWASTools
gwastools lrr baf NA
updated 8.5 years ago by ▴ 870 • written 8.5 years ago by ▴ 40
0
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5
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1.7k
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GWASTools assocTestCPH on cluster vs. computer
gwastools
updated 9.3 years ago by ▴ 870 • written 9.5 years ago by • 0
2
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3
replies
1.6k
views
Importing affymetrix genotype calls with GWASTools
gwastools genotype affymetrix microarrays
updated 8.6 years ago by ▴ 870 • written 8.6 years ago by ▴ 40
0
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2
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1.6k
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Errors when attempting to run association tests in GWASTools
gwastools
9.6 years ago mrynerson • 0
0
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1
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1.5k
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GWASTools instalation problem
GWASTools GWASTools
updated 9.9 years ago by ★ 8.2k • written 9.9 years ago by ▴ 10
0
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1
reply
1.5k
views
GWASTools for analyzing Canine_HD genotyping data
Organism cdf GWASTools Organism cdf GWASTools
11.2 years ago Stephanie M. Gogarten ▴ 870
0
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2
replies
1.5k
views
Question on 'gdsSubset' function
GWASTools
6.6 years ago yasuhito.nannya • 0
0
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3
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1.4k
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GWATools use in creating ncdf files
SNP cdf GWASTools SNP cdf GWASTools
updated 11.0 years ago by ▴ 60 • written 11.0 years ago by ▴ 870
0
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1
reply
1.4k
views
GWATools use in creating ncdf files
SNP Annotation cdf GWASTools SNP Annotation cdf GWASTools
updated 10.9 years ago by ▴ 870 • written 10.9 years ago by ▴ 60
1
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4
replies
1.4k
views
Errors when trying to install 'gwscat' on ubuntu with R 4.0.3
GWASTools gwascat
updated 3.5 years ago by ★ 6.5k • written 3.5 years ago by ▴ 10
0
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1
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1.3k
views
Error with FunciSNP
snp R gwastools
8.1 years ago musomilan • 0
0
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2
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1.3k
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GWASTools: assocTestRegression, forcing the analysis to use reference allele
GWASTools GWASTools
updated 9.8 years ago by ▴ 870 • written 9.8 years ago by ★ 13k
0
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2
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1.3k
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GWASTools mendelList Constructor
GWASTools GWASTools
updated 11.7 years ago by ▴ 870 • written 11.7 years ago by ▴ 60
0
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0
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1.2k
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A question about GWASTools package
cdf GWASTools cdf GWASTools
11.2 years ago Stephanie M. Gogarten ▴ 870
0
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0
replies
1.2k
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Fwd: GWASTools
cdf convert GWASTools cdf convert GWASTools
10.4 years ago Stephanie M. Gogarten ▴ 870
0
votes
1
reply
1.1k
views
Joint test for interactions in GWASTools
gwastools
updated 8.7 years ago by ▴ 870 • written 8.7 years ago by • 0
0
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1
reply
1.1k
views
SNP annotation
SNPRelate SNP GWASTools Annotation GWASdata
updated 2.3 years ago by ▴ 870 • written 2.5 years ago by • 0
2
votes
1
reply
1.1k
views
Error in importing signals with createAffyIntensityFile (GWASTools)
gwastools software error
updated 8.6 years ago by ▴ 870 • written 8.6 years ago by ▴ 40
0
votes
1
reply
1.1k
views
Using custom expected R to estimate LRR with GWASTools
gwastools
updated 8.3 years ago by ▴ 870 • written 8.3 years ago by ▴ 40
0
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0
replies
1.0k
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small GWASTools patch to allow to use already built gds objects in Genotype Readers
GWASTools GWASTools
10.1 years ago Karl Forner ▴ 70
0
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0
replies
1.0k
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GWASTools: Sandwich SE
GWASTools GWASTools
9.8 years ago Adrienne Stilp ▴ 30
0
votes
1
reply
909
views
GWASTools vcfWrite function
gwastools
6.0 years ago Stephanie M. Gogarten ▴ 870
0
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0
replies
884
views
GWATools use in creating ncdf files
cdf GWASTools cdf GWASTools
11.1 years ago Stephanie M. Gogarten ▴ 870
2
votes
4
replies
883
views
Question about GWASTools gdsSubset
GWASTools gdsSubset
written 15 months ago by • 0
1
vote
1
reply
812
views
Missing normalized x, normalized y, baf and logrrratio values
gwastools
updated 6.1 years ago by ▴ 870 • written 6.1 years ago by • 0
0
votes
1
reply
797
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using GENESIS R package with non-human species
genesis gwastools
3.8 years ago Stephanie M. Gogarten ▴ 870
0
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0
replies
512
views
Human to mouse SNP conversion
liftOver SNP GWASTools
14 months ago bonheur • 0
0
votes
2
replies
430
views
GENESIS: Can not use GdsGenotypeReader to read a gds file
GENESIS GWASTools GDSfile
updated 5 months ago by ▴ 870 • written 5 months ago by • 0
43 results • Page 1 of 1
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Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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