Moderator: Steve Lianoglou
Steve Lianoglou ♦ 12k
- Reputation:
- 11,630
- Status:
- Trusted
- Location:
- Genentech
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 day, 16 hours ago
- Joined:
- 7 years, 11 months ago
- Email:
- s*********@gmail.com
I am a Computational Biologist at Genentech working in Cancer Immunology.
In a previous life, I was studying alternative cleavage and polyadenylation in humans.
Posts by Steve Lianoglou
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... Awesome, thank you!
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written 1 day ago by
Steve Lianoglou ♦ 12k
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Comment:
C: Cross-species RNA-seq with DESeq2
... Perhaps you might try doing your alignments with salmon (or kallisto, license permitting) and using tximport to load up your results.
The tximport vignette shows you how to then import these data and summarize the transcript level counts to the gene level, as well as how you can incorporate the sam ...
written 11 days ago by
Steve Lianoglou ♦ 12k
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... We need to take a step back here and make sure that Biostrings installs correctly. You also need to provide more of R's error messages instead of your interpreted summary of what you think is going wrong.
For example, your "... says there is no Biostrings package" paraphrasing isn't exactly helpful ...
written 12 days ago by
Steve Lianoglou ♦ 12k
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... Restart and R and install it from a clean R session.
The message tells you that Biostrings is already loaded and it doesn't want to install a new version over it while it's in use.
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written 12 days ago by
Steve Lianoglou ♦ 12k
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... The downside to a homebrew installation is that you will have to compile every package by source, though, which can be a pain ...
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written 25 days ago by
Steve Lianoglou ♦ 12k
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... Not related to salmon, but why would the (R|F)PKM screw up your differential expression analysis when you used featureCounts?
I mean, if you ran featureCounts to get counts over your gene features, the most natural thing I could think of doing would be to then feed those counts directly into edgeR, ...
written 5 weeks ago by
Steve Lianoglou ♦ 12k
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... Some comment as before, you are missing a required package "RSQLite". You need to carefully read through the "Error:" messages you are getting and sort those out.
It's not clear to me how this happened, but your installation seems quite broken for one reason or another. When you start from a "clean ...
written 5 weeks ago by
Steve Lianoglou ♦ 12k
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91
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... It looks like you've somehow ended up with an incomplete installation because somehow somewhere someone is trying to load the matrixStats package, which doesn't appear to be installed.
Try installing that first, and try again.
install.packages("matrixStats")
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written 5 weeks ago by
Steve Lianoglou ♦ 12k
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187
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... Great, glad to hear that and thank you for taking the time to follow up and close the loop on this.
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written 5 weeks ago by
Steve Lianoglou ♦ 12k
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... You don't need (and can't use, AFAIK) trait data for module creation, so if your goal is to just identify modules of co-regulated genes, then your'e good.
Often people want to the associate the activation/expression-level of modules to "traits" but that's a downstream step ...
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written 7 weeks ago by
Steve Lianoglou ♦ 12k
Latest awards to Steve Lianoglou
Scholar
15 months ago,
created an answer that has been accepted.
For C: DEseq2 with limited gene set
Scholar
15 months ago,
created an answer that has been accepted.
For A: unable to find Lumi package in R
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For C: DEseq2 with limited gene set
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: edgeR subsetting DGEList by column/sample
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: Filtering lowly expressed genes in voom-limma analysis
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: Counting ambiguously mapped reads per feature
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: Filtering after a contrast
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: Perform limma on a subset of genes of interest
Scholar
15 months ago,
created an answer that has been accepted.
For A: unable to find Lumi package in R
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: Perform limma on a subset of genes of interest
Scholar
16 months ago,
created an answer that has been accepted.
For A: unable to find Lumi package in R
Guru
17 months ago,
received more than 100 upvotes.
Scholar
17 months ago,
created an answer that has been accepted.
For A: "Wobble" patterns for genome searching using Biostrings
Scholar
21 months ago,
created an answer that has been accepted.
For A: "Wobble" patterns for genome searching using Biostrings
Teacher
2.0 years ago,
created an answer with at least 3 up-votes.
For A: Perform limma on a subset of genes of interest
Teacher
2.0 years ago,
created an answer with at least 3 up-votes.
For A: Perform limma on a subset of genes of interest
Scholar
2.0 years ago,
created an answer that has been accepted.
For A: "Wobble" patterns for genome searching using Biostrings
Scholar
2.2 years ago,
created an answer that has been accepted.
For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
Scholar
2.3 years ago,
created an answer that has been accepted.
For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
Oracle
2.5 years ago,
created more than 1,000 posts (questions + answers + comments).
Voter
2.5 years ago,
voted more than 100 times.
Teacher
2.6 years ago,
created an answer with at least 3 up-votes.
For A: Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
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