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Recent Replies
Comment: Transcript identification and quantification
by
dsull
★
7.5k
AH perfect!! Thanks -- that's exactly right!
Here's the updated command (and links) for v3:
pip install kb_python
wget https://ra…
Comment: Gene Exons Painter
by
Mensur Dlakic
★
29k
I am really not picking up on you - really. It just strikes me that if you want to get people to use your tools, a little bit more effort i…
Answer: Assigning a string variable on Visual Studio using python
by
GenoMax
151k
Not sure what you are trying to do here. How are the two lines you wrote above connected? You can't have a space in python variable names, …
Comment: Transcript identification and quantification
by
GenoMax
151k
There are some barcodes provided here --> https://github.com/mortazavilab/parse_pipeline/tree/main/barcodes
Perhaps @dsull knows if there…
Comment: Ggplot make boxplots more wide
by
zx8754
12k
Set colour to Day as well:
```R
ggplot( data = metadata, aes(x = location, y = gene, fill = Day, colour = Day)) + geom_boxplot()
```
To …
Comment: Transcript identification and quantification
by
dsull
★
7.5k
Ooh, that's a bit tricky. I worked with v3 of the kit a while back but for some reason I can only find the R2/R3 barcodes. I'll let you kno…
Comment: The Biostar Herald for Monday, May 05, 2025
by
cmdcolin
★
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BinSeq format from ArcInstitute also ! https://github.com/ArcInstitute/binseq ...the trio of binseq+xsra+https://github.com/ArcInstitute/SR…
Comment: Transcript identification and quantification
by
anton.avramov
•
0
Thank you for your help. We’re using v3 chemistry—do you know where I can obtain the barcode sequences? I don’t believe Parse shares them d…
Comment: Transcript identification and quantification
by
anton.avramov
•
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Thanks for the reply! I do use Parse pipeline to get expression matrices but what I really want to do is to be able to identify the transcr…
Comment: About FastP Tool
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Look at your alignment file records (with `samtools view` and such) and check the 6th field (`CIGAR` strings are described on page 8 in SAM…
Comment: Ggplot make boxplots more wide
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Bastien Hervé
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https://ggplot2.tidyverse.org/reference/geom_dotplot.html
Comment: Ggplot make boxplots more wide
by
Nona
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How can I change it to a dot instead of a line?
Comment: Ggplot make boxplots more wide
by
Nona
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Yes its actually just one sample per location / day. Location is e.g. lung and liver and day is day 1,2,3 and gene is gene expression for …
Comment: Single cell demultiplexing using 10x and TotalSeq-B
by
tlallihuacan
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Hi @txemaheredia Did you find an answer? I'm having a similar problem with my own samples and I was wondering if its better to use HTOdemu…
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