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What are the difference between Seurat and Cell Ranger pipeline in processing single cell RNA-seq data

scrna-seq sequence leukemia rna-seq written 2.1 years ago by bwang258 • 20 • updated 2.1 years ago by Biostar ♦♦ 20

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a beginner question in RNA-seq workflow - what is the next step?

leukemia rna-seq written 3.5 years ago by galkimhi123 • 10

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Job: Cancer Genomics Post-Doctoral Position, The Ohio State University, Columbus, OH, USA

biostatistics cancer job genomics leukemia written 4.1 years ago by sucheston-campbell.1 • 10

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Recent Replies

C: How would I use BioPython to mass download some assemblies from NCBI? by genomax ♦ 90k
EDIT: Curiously using the fully qualified accession number (with version) works fine: $ ./da...
A: TCGA capture kits by markus.riester • 500
Yep, GDC provides that information. See here for a script to download it:https://github.com/lima1...
C: How would I use BioPython to mass download some assemblies from NCBI? by Istvan Albert ♦♦ 85k
What I find super irritating is that error message says: **invalid NCBI Assembly Accessions**. ...
A: TAIR Gene Symbols by Kevin Blighe ♦ 65k
Hey, There are two approaches here. 1, *org.At.tair.db* ----------------- You can use the ann...
C: How would I use BioPython to mass download some assemblies from NCBI? by genomax ♦ 90k
There is an explanation of what is excluded at the link you included above. So they are not doing...
C: How would I use BioPython to mass download some assemblies from NCBI? by Istvan Albert ♦♦ 85k
I have been looking at `datasets`. I am not too pleased with it so far, it feels like a half bake...
C: PCA plot, less points than samples by ATpoint ♦ 39k
You can try to increase the number of genes used for PCA, maybe use 1000 and hope they separate b...
C: PCA plot, less points than samples by eridanus • 0
thank you. I tried and it is 12. I thought about overlapping, but then I added the labels, and I ...
C: PCA plot, less points than samples by ATpoint ♦ 39k
Use `returnData=TRUE` for `plotPCA` and see whether there are 12 or 11 samples in the returned da...
A: How would I use BioPython to mass download some assemblies from NCBI? by genomax ♦ 90k
Since non-python solutions have been mentioned, consider [NCBI datasets][1]. It is the command li...
A: How would I use BioPython to mass download some assemblies from NCBI? by Istvan Albert ♦♦ 85k
No need to use Biopython. To mass download assemblies you can use the FTP site (note the links t...
A: How would I use BioPython to mass download some assemblies from NCBI? by JC ♦ 11k
[Entrez tools][1] can be used to avoid coding. [1]: https://www.ncbi.nlm.nih.gov/books/NBK179...

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