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Job:
Postdoc on integrating and analyzing new transcriptome types in the Bgee database
rnaseq
data integration
single-cell
pacbio
across species
Job
4.4 years ago
bgee
• 0
2
votes
5
replies
1.2k
views
Gviz - display/indicate soft-clipped bases - indicate supplementary alignments
gviz
bam
pacbio
updated 6.2 years ago by
florian.hahne@novartis.com
★ 1.6k • written 6.2 years ago by
thackl
• 0
0
votes
1
reply
824
views
How to read in PacBio .bam.pbi file
pacbio
pbi
4.3 years ago
Frocha
▴ 10
4
votes
3
replies
800
views
The ShortRead package does not handle quality score '~' (Q=93) found in PacBio fastq files
shortread
pacbio
fastq
updated 4.5 years ago by
Martin Morgan
25k • written 4.5 years ago by
benjamin.j.callahan
▴ 50
4 results • Page
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Comment: using DESeq2 for ATAC analyses
by
eric.kern13
▴ 10
To expand on what's written here: deseq2 can achieve roughly constant variance $C$ across genes by setting the per-gene dispersion $\phi_j$…
Comment: TPM normalization starting with read counts
by
ATpoint
★ 1.4k
Neither edgeR nor DESeq2 output TPM directly. TPM is easy to calculate though if counts and appropriate length info is available (https://s…
Comment: error running UniProt.ws
by
davi.vuko
• 0
I still get the same result as above, should running BiocManager::install() do the trick?
Answer: Adding custom transcript to Salmon index
by
ATpoint
★ 1.4k
Yes, you would add the sequence to the reference transcriptome that is used for the gentrome construction. Simply make a separate fasta fil…
Comment: IsoformSwitchAnalyzeR package on mouse data
by
bpshtiwan
▴ 10
Hello Ryan, Also, I am not able to find esemble file that has haplotype info in it. Kindly, have you solved the problem? Best
Votes
A: Importance of Order in Design Formula
remove microarray batch effects using Limma
On empirical Bayes of edgeR
Answer: CQN to DESeq2
Comment: package 'BiocInstaller' is not available (for R version 3.4.4)
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