Showing : DNAstringset • reset
1
vote
5
replies
4.3k
views
Converting a DNAStringSetList to characters quickly
readVcf DNAStringSet DNAStringSetList variantannotation readvcf
9.0 years ago dan.gatti • 0
3
votes
8
replies
1.7k
views
problem with @ranges@start in DNAStringSet
vcf testthat dnastringset
8.5 years ago TimothéeFlutre ▴ 80
6
votes
6
replies
5.1k
views
how to extract part of the DNA sequences from a DNAstringset
DNAstringset
updated 7.2 years ago by 16k • written 7.2 years ago by ▴ 20
0
votes
2
replies
835
views
how to deal with multiple barcodes/index in the analysis
dnastringset aastringset
7.2 years ago XIA.PAN ▴ 20
3
votes
4
replies
3.7k
views
How to convert a DnaStringSet object to list of seq?
dnastringset list stringset
updated 6.8 years ago by 25k • written 6.8 years ago by ▴ 50
15
votes
2
replies
17k
views
Extract sequence from DNAStringSet object
dnastringset
updated 8.5 years ago by 25k • written 8.5 years ago by ▴ 120
2
votes
1
reply
787
views
DNAStringSet to DNAStringSetList according to pattern in sequence names
dnastringset dnastringsetlist seqnames
5.5 years ago s.ghignone ▴ 10
0
votes
3
replies
1.1k
views
I want to sample (random ) nucleic acids at middle 20 positions of DNAstring set
DNAStringSet sample
updated 8.4 years ago by 16k • written 8.4 years ago by ▴ 50
2
votes
3
replies
1.7k
views
visualing pwm motif on a DNAstring
pwmenrich dnastringset
updated 8.1 years ago by ▴ 50 • written 8.1 years ago by ▴ 20
3
votes
1
reply
5.3k
views
extract subsequence(s) from DNAStringSet with getSeq
dnastringset getseq
updated 7.8 years ago by 16k • written 7.8 years ago by ▴ 80
2
votes
5
replies
4.4k
views
How to use subSeq with DNAStringSet and information of GroupedIRanges?
subseq Xvector dnastringset
updated 6.9 years ago by 16k • written 6.9 years ago by • 0
0
votes
4
replies
1.4k
views
Using iterators and foreach with doMC, using DNAStringSets
dnastringset parallel iterators
8.4 years ago ben.ward ▴ 30
12 results • Page 1 of 1
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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