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SNPs
•
reset
1
vote
2
replies
1.8k
views
Any tool to calculate Fst on haploid data?
snps
VCF
updated 9 months ago by
Arafat
• 0 • written 5.9 years ago by
rkdonthu
▴ 10
0
votes
1
reply
245
views
Error running hierClust
hierClust
R
SNPs
clustering
updated 10 months ago by
James W. MacDonald
62k • written 10 months ago by
sekhwal
• 0
0
votes
0
replies
431
views
How to extract genomic positions of SNPs using snp-sites or using any R package?
SNPs
3.9 years ago
pltbiotech_tkarthi
• 0
0
votes
0
replies
816
views
vcf to venn diagram
snps
vcf
venn diagram
ggplot2
4.1 years ago
mictadlo
▴ 10
0
votes
6
replies
793
views
Physical position to gene positions
bioconductor
molecular biology
snps
updated 4.2 years ago by
James W. MacDonald
62k • written 4.2 years ago by
jebreen20
• 0
2
votes
5
replies
1.8k
views
Error with R package motifbreakR while trying to read a vcf file with snps.from.file function
motifbreakR
vcf
snps
motif analysis
updated 4.6 years ago by
Valerie Obenchain
★ 6.7k • written 4.6 years ago by
svlachavas
▴ 800
3
votes
4
replies
1.0k
views
No annotation for single SNPs
variantannotation
SNPs
txdb.hsapiens.ucsc.hg19.knowngene
ucsc
updated 5.6 years ago by
Valerie Obenchain
★ 6.7k • written 5.6 years ago by
Lna
• 0
0
votes
1
reply
1.1k
views
Extract SNPs and INDELs
hsapiens
snps
indels
updated 7.2 years ago by
Hervé Pagès
16k • written 7.2 years ago by
kredens
• 0
0
votes
1
reply
1.1k
views
Counting SNPs where ambiguity codes represent heterozygosity.
Biostrings
SNPs
alignment
updated 7.5 years ago by
Hervé Pagès
16k • written 7.6 years ago by
ben.ward
▴ 30
0
votes
4
replies
1.4k
views
Marking and annotating several SNPs on Ideogram track by Gviz package.
gviz
ideogram
snps
updated 8.0 years ago by
florian.hahne@novartis.com
★ 1.6k • written 8.0 years ago by
vnyirongo
• 0
4
votes
3
replies
1.6k
views
Overlap the snps
overlap
snps
granges
iranges
updated 8.3 years ago by
Michael Lawrence
11k • written 8.3 years ago by
anastasiya-terskih
▴ 10
11 results • Page
1 of 1
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Replies
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…
Answer: Which genes are outliers in DESeq2?
by
Michael Love
39k
Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…
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
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to
Ryan
• 0
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to
Guido Hooiveld
★ 3.5k
Scholar
to
James W. MacDonald
62k
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to
Michael Love
39k
Popular Question
to
twtoal
▴ 10
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