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SNPs
•
reset
1
vote
2
replies
3.5k
views
Any tool to calculate Fst on haploid data?
snps
VCF
updated 3.5 years ago by
Arafat
• 0 • written 8.7 years ago by
rkdonthu
▴ 10
0
votes
1
reply
912
views
Error running hierClust
hierClust
R
SNPs
clustering
updated 3.6 years ago by
James W. MacDonald
68k • written 3.6 years ago by
sekhwal
• 0
0
votes
0
replies
1.3k
views
How to extract genomic positions of SNPs using snp-sites or using any R package?
SNPs
6.6 years ago
pltbiotech_tkarthi
• 0
0
votes
0
replies
1.6k
views
vcf to venn diagram
snps
vcf
venn diagram
ggplot2
6.8 years ago
mictadlo
▴ 10
0
votes
6
replies
1.7k
views
Physical position to gene positions
bioconductor
molecular biology
snps
updated 6.9 years ago by
James W. MacDonald
68k • written 6.9 years ago by
jebreen20
• 0
2
votes
5
replies
3.2k
views
Error with R package motifbreakR while trying to read a vcf file with snps.from.file function
motifbreakR
vcf
snps
motif analysis
updated 7.4 years ago by
Valerie Obenchain
★ 6.8k • written 7.4 years ago by
svlachavas
▴ 840
3
votes
4
replies
1.9k
views
No annotation for single SNPs
variantannotation
SNPs
txdb.hsapiens.ucsc.hg19.knowngene
ucsc
updated 8.3 years ago by
Valerie Obenchain
★ 6.8k • written 8.4 years ago by
Lna
• 0
0
votes
1
reply
1.8k
views
Extract SNPs and INDELs
hsapiens
snps
indels
updated 9.9 years ago by
Hervé Pagès
16k • written 9.9 years ago by
kredens
• 0
0
votes
1
reply
2.0k
views
Counting SNPs where ambiguity codes represent heterozygosity.
Biostrings
SNPs
alignment
updated 10.3 years ago by
Hervé Pagès
16k • written 10.3 years ago by
ben.ward
▴ 30
0
votes
4
replies
2.3k
views
Marking and annotating several SNPs on Ideogram track by Gviz package.
gviz
ideogram
snps
updated 10.8 years ago by
florian.hahne@novartis.com
★ 1.6k • written 10.8 years ago by
vnyirongo
• 0
4
votes
3
replies
2.7k
views
Overlap the snps
overlap
snps
granges
iranges
updated 11.1 years ago by
Michael Lawrence
★ 11k • written 11.1 years ago by
anastasiya-terskih
▴ 10
11 results • Page
1 of 1
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis
by
piffelpaff
▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis
by
Michael Love
43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Votes
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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