Admin: nitesh.turaga

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nitesh.turaga140
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Posts by nitesh.turaga

<prev • 27 results • page 1 of 3 • next >
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Comment: C: bug in "dispersion" argument in edgeR - rpkmByGroup
... If you are able to use `docker`, and not worry about system dependencies, In a `Dockerfile` ``` FROM bioconductor/bioconductor_full:RELEASE_3_9 RUN R -e "BiocManager::install('edgeR') ``` Then build, ``` docker build -t bioc-edgeR:latest -f /Dockerfile ``` Use ``` docker run -it bioc-edgeR:la ...
written 3 months ago by nitesh.turaga140
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Comment: C: bug in "dispersion" argument in edgeR - rpkmByGroup
... I am able to reproduce this error using `conda create --name edgeRenv bioconductor-edger`. It seems that Bioconda uses R from conda-forge (right now it uses R-3.5.1), and they are waiting for R-3.6.1 to be released before updating to that. This seems to be caused by the way Bioconda maintainers de ...
written 3 months ago by nitesh.turaga140
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Comment: C: Seeking help deploying Shiny application to RStudio Connect with Bioconductor pa
... Hi, It seems like your packrat environment is trying to use R-3.5.2 but your R version on the Rstudio connect is R-3.6.0. But besides that, I think there are some missing system dependencies on your RStudio connect server, and you might have to ask your system admin to install those dependencies f ...
written 3 months ago by nitesh.turaga140
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Comment: C: ensemblVEP: "Ensembl VEP is not installed in your path."
... Hi, Is your goal here to use `ensemblVEP` as a package inside a Docker image? Or is it to build your own Docker image which uses bioconda to install `ensembleVEP`? If it is the first one, then I suggest you use a different base image, (this is a temporary suggestion) ``` FROM bioconductor/bioc ...
written 7 months ago by nitesh.turaga140
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Comment: C: List of Deprecated Package Bioc 3.9
... Package `miRsponge` has been deprecated in favor of `miRspongeR`. This is a name change as requested by the maintainer. ...
written 7 months ago by nitesh.turaga140
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Answer: C: Installing BiocParallel package on R.3.4.4
... Please try installing via `biocLite()` which is the Bioconductor recommended way of installing bioconductor packages in R-3.4 ``` source("https://bioconductor.org/biocLite.R") BiocInstaller::biocLite("BiocParallel") ``` https://www.bioconductor.org/install/#Legacy (check out this link for more inf ...
written 7 months ago by nitesh.turaga140
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Comment: C: MAGeCKFlute - Installation
... You have a trailing `)` which doesn't work try this, ``` conda create --name mageck-vispr mageck mageck-vispr python=3 ``` But make sure you have your conda channels set correctly (as given by the bioconda page) Also, it's taking a while on my machine as well. But, i suggest you contact, https: ...
written 7 months ago by nitesh.turaga140
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Comment: C: How can I install DeSeq2 in Jupyter Notebook?
... Hi, It's worth taking a look at Bioconda in this instance. I feel like once you launch a Jupyter notebook. If you have anaconda installed already, and you are trying to to install DESeq2, make sure the list of channels you have set are correct. ``` conda config --add channels defaults conda confi ...
written 7 months ago by nitesh.turaga140
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Answer: A: DEXSeqHTML getListElement GRanges error
... Hi Lance, I guess you can install bioconductor-dexseq==1.24.0 on a new conda environment, and copy the script being run from the tool, and use it within that conda environment? AS you mentioned the script being run is /galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/dexseq/f89c9b25feb4/dexseq/ ...
written 10 months ago by nitesh.turaga140
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Comment: C: Can't push upstream - duplicate commits
... Hi Sam, I took a look at bumphunter. There are a couple of things I wanted to say. First, it seems like this commit was the one creating all the duplicate commits for the package. 718d3d8 Merge with Bioconductor devel brach $$ git show 718d3d8 commit 718d3d87af114f8dc404c3889c673fac861bb84c ...
written 11 months ago by nitesh.turaga140

Latest awards to nitesh.turaga

Appreciated 2.6 years ago, created a post with more than 5 votes. For Bioconductor git server is now LIVE!
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Bioconductor git transition BETA phase starts now.
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Bioconductor git server is now LIVE!
Scholar 2.6 years ago, created an answer that has been accepted. For A: Access to github repository- how does one know if their ssh public key was accep
Scholar 2.6 years ago, created an answer that has been accepted. For A: Remote rejected after resetting to previous commit

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