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snpstats
•
reset
1
vote
2
replies
835
views
Error in ld(): STRING_ELT() can only be applied to a 'character vector', not a 'NULL'
ld()
snpStats
14 months ago
Anastasiia
• 0
0
votes
0
replies
374
views
Extract flanking sequences SNP without reference genome
SNPData
snpStats
SNP
flankingsequences
22 months ago
Amber
• 0
0
votes
0
replies
295
views
Coercion of a numeric matrix into a SnpMatrix
snpStats
3.0 years ago
schandry
• 0
0
votes
1
reply
522
views
GWAS: access Imputation probabilities: snpStats
gwas
snpstats
GWAS
Imputation
snpStats
4.6 years ago
GENOMIC_region
• 0
1
vote
1
reply
850
views
reading ped error when using the snpStats library
snpstats
ped file
R
5.3 years ago
kzelaya2
▴ 10
0
votes
0
replies
754
views
snp.rhs.estimates and/or .tests and extracting results
snpStats
additive model
5.9 years ago
natalie.jean.mcdonald
• 0
1
vote
0
replies
754
views
Error when computing ld with snpStats in big samples
software error
snpstats
`ld
6.7 years ago
carlos.ruiz
• 0
1
vote
1
reply
1.2k
views
Write the "map" DataFrame from genotypeToSnpMatrix() to a text file
variantannotation
DataFrame
snpstats
7.2 years ago
TimothéeFlutre
▴ 80
1
vote
2
replies
1.3k
views
Automatic NA values generated by the ld() function of snpStats package
snpStats
BioConductor
LD
Linkage Disequilibrium
NA
8.0 years ago
remi.tournebize
▴ 10
0
votes
1
reply
994
views
snp analysis GWAS
snpstats
updated 8.2 years ago by
Steve Lianoglou
13k • written 8.2 years ago by
ahmadamareen1985
• 0
0
votes
0
replies
1.3k
views
(snpStats) Error: Error in terms.formula(formula, special, data = data) : invalid term in model formula
software error
snpStats
8.2 years ago
vickygarfield87
• 0
0
votes
0
replies
748
views
Are the 'trait' and 'phenotype' objects in the snpStats snp.rhs.estimates command the same thing?
snpStats
8.2 years ago
vickygarfield87
• 0
0
votes
1
reply
1.2k
views
snpStats reference allele used in genetic associations?
SNP
Category
snpStats
SNP
Category
snpStats
updated 8.7 years ago by
Vincent J. Carey, Jr.
6.6k • written 8.7 years ago by
Guest User
★ 12k
0
votes
3
replies
1.3k
views
Error reading imputed file using snpStats package
SNP
snpStats
SNP
snpStats
updated 9.0 years ago by
Vincent J. Carey, Jr.
6.6k • written 9.0 years ago by
francesca casalino
▴ 50
0
votes
1
reply
1.3k
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
9.2 years ago
David Winsemius
▴ 40
0
votes
0
replies
1.7k
views
Plink Data for Fst Calculations
snpStats
snpStats
9.2 years ago
Voke AO
▴ 760
0
votes
3
replies
824
views
SNPstats package bug report
snpStats
snpStats
9.2 years ago
Guest User
★ 12k
0
votes
0
replies
1.4k
views
snpStats/GWASTools conversion
cdf
convert
snpMatrix
snpStats
GWASTools
cdf
convert
snpMatrix
snpStats
GWASTools
9.3 years ago
Stephanie M. Gogarten
▴ 820
0
votes
0
replies
923
views
snpStats Fst Implementation
snpStats
snpStats
9.4 years ago
Voke AO
▴ 760
0
votes
1
reply
1.1k
views
col.summary error in snpStats
SNP
Sequencing
Annotation
snpMatrix
snpStats
SNP
Sequencing
Annotation
snpMatrix
snpStats
updated 9.9 years ago by
Vincent J. Carey, Jr.
6.6k • written 9.9 years ago by
Tereza Jezkova - personal
▴ 10
0
votes
1
reply
937
views
snpStats --- MAF in Pedigrees
snpStats
snpStats
updated 10.1 years ago by
Vincent J. Carey, Jr.
6.6k • written 10.1 years ago by
Samuel Younkin
▴ 60
0
votes
0
replies
757
views
statistics from snpStats objects
SNP
snpStats
SNP
snpStats
10.7 years ago
james power
▴ 10
0
votes
3
replies
2.3k
views
GWAS with Affymetrix SNP 6.0
SNP
oligo
snpMatrix
snpStats
SNP
oligo
snpMatrix
snpStats
updated 10.7 years ago by
Vincent J. Carey, Jr.
6.6k • written 10.7 years ago by
David Hervás
▴ 20
0
votes
4
replies
1.2k
views
snpStats, read.long, alleles in two columns
SNP
Genetics
snpStats
SNP
Genetics
snpStats
updated 10.9 years ago by
David Clayton
▴ 20 • written 10.9 years ago by
Liz Hare
▴ 30
0
votes
2
replies
1.1k
views
Weird error when installing VariantAnnotation and/or snpStats (whether from SVN or using biocLite)
snpStats
snpStats
updated 11.3 years ago by
Martin Morgan
25k • written 11.3 years ago by
Tim Triche
★ 4.2k
25 results • Page
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Comment: mas5calls function doesn't work; mirna40cdf problem
by
Berna
• 0
Thanks for all answers. I have tried, but still get an error message. Do you know how I can work around this? > library(pd.mir…
Answer: struggling to create a heatmap
by
ATpoint
★ 2.1k
I am reluctant to read through that wall of code. Here is what would work. Note that prefiltering makes sense before, not after running `DE…
Answer: collapseReplicates error after tximeta
by
Michael Love
39k
The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
by
ATpoint
★ 2.1k
That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
Answer: Which genes are outliers in DESeq2?
by
ATpoint
★ 2.1k
You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…
Votes
Significant reporter activity with mpralm function
Answer: I cannot install annotables package in Rstudio (macOS)
Answer: log2 of normalized counts for further analyzes
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
Awards
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Commentator
to
Lucia
▴ 40
Popular Question
to
Ryan
• 0
Popular Question
to
Guido Hooiveld
★ 3.5k
Scholar
to
James W. MacDonald
62k
Commentator
to
Michael Love
39k
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