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snpStats
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0
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4
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1.5k
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snpStats, read.long, alleles in two columns
SNP
Genetics
snpStats
SNP
Genetics
snpStats
updated 12.2 years ago by
David Clayton
▴ 20 • written 12.2 years ago by
Liz Hare
▴ 30
0
votes
3
replies
1.1k
views
SNPstats package bug report
snpStats
snpStats
10.4 years ago
Guest User
★ 13k
0
votes
3
replies
2.8k
views
GWAS with Affymetrix SNP 6.0
SNP
oligo
snpMatrix
snpStats
SNP
oligo
snpMatrix
snpStats
updated 11.9 years ago by
Vincent J. Carey, Jr.
6.7k • written 11.9 years ago by
David Hervás
▴ 20
0
votes
3
replies
1.7k
views
Error reading imputed file using snpStats package
SNP
snpStats
SNP
snpStats
updated 10.3 years ago by
Vincent J. Carey, Jr.
6.7k • written 10.3 years ago by
francesca casalino
▴ 50
0
votes
2
replies
1.4k
views
Weird error when installing VariantAnnotation and/or snpStats (whether from SVN or using biocLite)
snpStats
snpStats
updated 12.6 years ago by
Martin Morgan
25k • written 12.6 years ago by
Tim Triche
★ 4.2k
1
vote
2
replies
1.8k
views
Automatic NA values generated by the ld() function of snpStats package
snpStats
BioConductor
LD
Linkage Disequilibrium
NA
9.2 years ago
remi.tournebize
▴ 10
1
vote
2
replies
1.3k
views
Error in ld(): STRING_ELT() can only be applied to a 'character vector', not a 'NULL'
ld()
snpStats
2.4 years ago
Anastasiia
• 0
0
votes
1
reply
1.6k
views
[R] freetype 2.5.2, problem with the survival package, build R 2.15.x with gcc 4.8.x
Regression
Survival
snpStats
Regression
Survival
snpStats
10.4 years ago
David Winsemius
▴ 40
1
vote
1
reply
1.6k
views
Write the "map" DataFrame from genotypeToSnpMatrix() to a text file
variantannotation
DataFrame
snpstats
8.5 years ago
TimothéeFlutre
▴ 80
0
votes
1
reply
1.3k
views
snpStats --- MAF in Pedigrees
snpStats
snpStats
updated 11.3 years ago by
Vincent J. Carey, Jr.
6.7k • written 11.3 years ago by
Samuel Younkin
▴ 60
1
vote
1
reply
1.2k
views
reading ped error when using the snpStats library
snpstats
ped file
R
6.5 years ago
kzelaya2
▴ 10
0
votes
1
reply
934
views
GWAS: access Imputation probabilities: snpStats
gwas
snpstats
GWAS
Imputation
snpStats
5.8 years ago
GENOMIC_region
• 0
0
votes
1
reply
1.3k
views
snp analysis GWAS
snpstats
updated 9.4 years ago by
Steve Lianoglou
★ 13k • written 9.4 years ago by
ahmadamareen1985
• 0
0
votes
1
reply
1.4k
views
col.summary error in snpStats
SNP
Sequencing
Annotation
snpMatrix
snpStats
SNP
Sequencing
Annotation
snpMatrix
snpStats
updated 11.1 years ago by
Vincent J. Carey, Jr.
6.7k • written 11.1 years ago by
Tereza Jezkova - personal
▴ 10
0
votes
1
reply
1.6k
views
snpStats reference allele used in genetic associations?
SNP
Category
snpStats
SNP
Category
snpStats
updated 10.0 years ago by
Vincent J. Carey, Jr.
6.7k • written 10.0 years ago by
Guest User
★ 13k
0
votes
0
replies
607
views
Coercion of a numeric matrix into a SnpMatrix
snpStats
4.2 years ago
schandry
• 0
0
votes
0
replies
1.8k
views
snpStats/GWASTools conversion
cdf
convert
snpMatrix
snpStats
GWASTools
cdf
convert
snpMatrix
snpStats
GWASTools
10.6 years ago
Stephanie M. Gogarten
▴ 870
0
votes
0
replies
1.1k
views
snpStats Fst Implementation
snpStats
snpStats
10.6 years ago
Voke AO
▴ 760
0
votes
0
replies
2.0k
views
Plink Data for Fst Calculations
snpStats
snpStats
10.4 years ago
Voke AO
▴ 760
0
votes
0
replies
1.0k
views
statistics from snpStats objects
SNP
snpStats
SNP
snpStats
11.9 years ago
james power
▴ 10
0
votes
0
replies
1.0k
views
Are the 'trait' and 'phenotype' objects in the snpStats snp.rhs.estimates command the same thing?
snpStats
9.5 years ago
vickygarfield87
• 0
0
votes
0
replies
1.7k
views
(snpStats) Error: Error in terms.formula(formula, special, data = data) : invalid term in model formula
software error
snpStats
9.5 years ago
vickygarfield87
• 0
0
votes
0
replies
730
views
Extract flanking sequences SNP without reference genome
SNPData
snpStats
SNP
flankingsequences
3.1 years ago
Amber
• 0
1
vote
0
replies
1.1k
views
Error when computing ld with snpStats in big samples
software error
snpstats
`ld
7.9 years ago
carlos.ruiz
• 0
0
votes
0
replies
1.0k
views
snp.rhs.estimates and/or .tests and extracting results
snpStats
additive model
7.2 years ago
natalie.jean.mcdonald
• 0
25 results • Page
1 of 1
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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