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Workshop recording from NYU Langone Medical Center on Machine Learning for Transcriptomics data
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Recent Replies
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A: GATK DP filter for multiple samples by
Flávia Rogério • 0
I have exactly the same question about DP filter. Did you find some way to filter it?
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C: High no feature counts in ht-seq counts by
genomax ♦ 59k
I think this is a point where access to your data/analysis may be needed to figure out what is go...
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C: How to export rld (rlog) or vsd values from DESeq2? by
LuisNagano • 10
I tried, but happens that error: rld <- rlog(dds, blind=FALSE) write.csv(rld, file="r...
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C: Interpretation of TCGA clinical data by
Charles Warden ♦ 5.8k
Python has some XML (and JSON) libraries that can be imported, which you might find helpful: htt...
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C: Finding SNV showing allele specific bias by
ishmahe16 • 0
So i had 6 files 3 control and 3 primed files and had to find the most differentially expressed g...
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C: High no feature counts in ht-seq counts by
eozcan • 0
I tried another annotation file and a fasta file from Ensemle, the previous one from ncbi. In ord...
-
C: How to export rld (rlog) or vsd values from DESeq2? by
WouterDeCoster ♦ 35k
And what about something like rld <- rlog(dds, blind=FALSE) write.csv(rld, file="rld....
-
C: umi_tools extract error: IndexError: string index out of range by
genomax ♦ 59k
Please start a new thread if you have a new question.
-
C: How to export rld (rlog) or vsd values from DESeq2? by
LuisNagano • 10
Thank you, WouterDeCoster, but i don't want to apply the functions "rlog" or "vst", I just did th...
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C: High no feature counts in ht-seq counts by
genomax ♦ 59k
Only thing I can think of is the annotation file you downloaded is either not in the correct form...
-
C: High no feature counts in ht-seq counts by
eozcan • 0
I tried that it does not change/improve my reads.
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A: umi_tools extract error: IndexError: string index out of range by
Rituriya • 20
Hi again, If I followed UMI extraction first and then adapter trimming later, there is a weird l...
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