User: Michael Steinbaugh

Reputation:
40
Status:
New User
Location:
Constellation Pharmaceuticals
Website:
https://steinbaugh.com/
Twitter:
mjsteinbaugh
Scholar ID:
Google Scholar Page
Last seen:
1 day, 22 hours ago
Joined:
3 years, 4 months ago
Email:
m***@steinbaugh.com

Posts by Michael Steinbaugh

<prev • 27 results • page 1 of 3 • next >
0
votes
0
answers
54
views
0
answers
Comment: C: Bioconductor Devel 3.11 Notification
... Is there a rough estimate for the R 4.0 release date yet? ...
written 9 days ago by Michael Steinbaugh40
0
votes
1
answer
74
views
1
answers
Comment: C: Unable to install RBGL in Bioconductor 3.10 release
... OK I posted a temporary fix on GitHub, but the automatic configuration needs to be updated to support RHEL 7. ...
written 20 days ago by Michael Steinbaugh40
1
vote
1
answer
74
views
1
answer
Unable to install RBGL in Bioconductor 3.10 release
... Hi all, I'm hitting an RBGL installation issue on RHEL 7 for Bioconductor 3.10, in case anybody else see this. I filed a related issue over on GitHub: https://github.com/Bioconductor/RBGL/issues/2 ```R BiocManager::install("RBGL") ``` ``` Bioconductor version 3.10 (BiocManager 1.30.9), R 3.6.1 (2 ...
rbgl bh written 20 days ago by Michael Steinbaugh40 • updated 20 days ago by Martin Morgan ♦♦ 24k
0
votes
1
answer
306
views
1
answers
Comment: C: tximport transcript missing
... Also, a bit unrelated but potentially relevant: [bcbio-nextgen](https://bcbio-nextgen.readthedocs.io/) supports salmon and kallisto, and will output a correct tx2gene.csv mapping file automatically. Our [bcbioRNASeq](https://bioinformatics.sph.harvard.edu/bcbioRNASeq/) R package will parse this outp ...
written 6 weeks ago by Michael Steinbaugh40
0
votes
1
answer
306
views
1
answers
Comment: C: tximport transcript missing
... Great tip ag1805x. I added a modified version of this shell script to my koopa library, which outputs a tx2gene.csv file: https://github.com/acidgenomics/koopa/blob/master/bin/tx2gene-from-ensembl-fasta ...
written 6 weeks ago by Michael Steinbaugh40
0
votes
1
answer
167
views
1
answers
Comment: C: Correct way to split and unsplit a DataFrame
... Perfect, thanks Michael! ...
written 12 weeks ago by Michael Steinbaugh40
0
votes
1
answer
167
views
1
answers
Comment: C: Correct way to split and unsplit a DataFrame
... The `stack()` function also gets close but doesn't unsplit back to the original `DataFrame` unmodified: ``` help(topic = "SplitDataFrameList", package = "IRanges") stack(x = split, index.var = ".idx") ``` ``` DataFrame with 4 rows and 3 columns .idx a b C a 3 ...
written 12 weeks ago by Michael Steinbaugh40
1
vote
1
answer
167
views
1
answer
Correct way to split and unsplit a DataFrame
... I'm having trouble splitting and unsplitting a `DataFrame`, using the methods defined in IRanges. Here's an attempt at a minimal reprex. ```r library(IRanges) df <- DataFrame( a = seq_len(4L), b = as.factor(rep(c("b", "a"), each = 2L)), row.names = LETTERS[seq_len(4L)] ) print(df) `` ...
iranges s4vectors written 12 weeks ago by Michael Steinbaugh40 • updated 12 weeks ago by Michael Lawrence11k
0
votes
1
answer
250
views
1
answers
Comment: C: Install Bioconductor 3.7
... It could be an issue specific to rocker/r-ver. Here's a minimal reproducible example. Dockerfile: ``` FROM rocker/r-ver:3.5.3 WORKDIR /tmp ADD install.R . RUN R -f install.R WORKDIR / ``` Corresponding install.R file: ``` install.packages("BiocManager") BiocManager::install(version = "3.7") ``` ...
written 6 months ago by Michael Steinbaugh40
0
votes
1
answer
250
views
1
answers
Comment: C: Install Bioconductor 3.7
... I copied the error from my Docker build, see below ...
written 6 months ago by Michael Steinbaugh40

Latest awards to Michael Steinbaugh

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 377 users visited in the last hour