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Recent Replies
Answer: Problem running interproscan-5.15-54.0 for protein sequences
by
Pratyay
•
0
Hi, can you guide me how to compile the src folder?
Many thanks!
Comment: Matching gene-expression data with clinical data: best practices.
by
krushnach80
★
1.1k
You can check [this][1]
[1]: https://www.linkedomics.org/
Answer: Matching gene-expression data with clinical data: best practices.
by
jose.sgomez94
•
0
Figured out one can use the TCGAutils package in R and UUIDtobarcode() function. Still, suggestions of best practices would be awesome!
Answer: Understanding multifactor designs and control variables in DESeq2
by
FrankStarling
▴
50
https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2021/RNAseq/Markdowns/10_DE_analysis_with_DESeq2.Solutions.html
…
Comment: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ?
by
Adaline.D
•
0
I appreciate your help, LChart! I will use raw data in case of a substantial loss of power.
(1) The publication did a PCA and then analy…
Answer: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ?
by
LChart
2.2k
Short answer: use LIMMA
Long answer: edgeR uses a negative binomial model, and expects *counts* and not *values*. Please read section 2.8.…
Comment: Python formatting when visualizing Primer3-py dimers
by
bhumm
▴
30
Wayne, both of these methods work beautifully. I really appreciate the detail you provided, thank you so much for your help!
Comment: Ortholog assembly and extraction
by
dthorbur
▴
420
I really like `orthofinder` and use it frequently, but there are also plenty of other tools out there. [Here](https://academic.oup.com/mbe/…
Answer: Cellranger sequencing
by
ATpoint
70k
Not that I am aware of. Unlike methods such as salmon it does genome alignment and does not resolve the exact transcript expression composi…
Answer: Assembly at lineage level from shotgun data ?
by
Mensur Dlakic
★
23k
The paper I list below is meant for improving the existing MAG assemblies. Yet the program will do what you want: if you give it a referenc…
Comment: Ortholog assembly and extraction
by
GenoMax
127k
Many seem to use `orthofinder` for this purpose. See if it is useful: https://github.com/davidemms/OrthoFinder
Answer: Python formatting when visualizing Primer3-py dimers
by
Wayne
★
1.7k
Try this so you'll see that using [tabulate](https://github.com/astanin/python-tabulate) to print the dataframe causes it to respect the li…
Comment: Python formatting when visualizing Primer3-py dimers
by
bhumm
▴
30
Glad I am making this more clear. The 'test1' in practice will be the 'primer name' to allow for tracking of other metrics (Tm, hairpin str…
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