User: Ashish Jain

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Posts by Ashish Jain

<prev • 11 results • page 1 of 2 • next >
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Answer: A: can TissueEnrich be used to calculate the tissue-specific lncRNAs in plants?
... Hi Carina, Thank you for your interest in our tool. As you know, we only have data protein coding genes data and it doesn't have information about the lncRNAs. However, if you want to explore more about the tissue-specific lncRNAs and you have the lncRNAs data from different tissues, you can always ...
written 11 weeks ago by Ashish Jain0
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Answer: A: Overall genes number in the TissueEnrich package output
... Hi, In TissueEnrich, we are dividing the genes into six different groups which are specified in our paper (http://doi.org/10.1093/bioinformatics/bty890). The 36 genes could be in the other three non-tissue specific gene groups (Not Expressed, Expressed In all, or Mixed). You can also confirm that b ...
written 6 months ago by Ashish Jain0
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Answer: A: How to handle replicates and treatment conditions in TissueEnrich package
... Hi Andrew, As from your description, it seems like you are trying to find the differentially expressed genes based on the drug treatment. I recommend that you should use tools like DESeq2 or edgeR for that. Also, we took care of replicates by taking the average of the gene expression across replica ...
written 7 months ago by Ashish Jain0
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Comment: C: How to handle replicates and treatment conditions in TissueEnrich package
... Hi Andrew, As from your description, it seems like you are trying to find the differentially expressed genes based on the drug treatment. I recommend that you should use tools like DESeq2 or edgeR for that. Also, we took care of replicates by taking the average of the gene expression across replica ...
written 7 months ago by Ashish Jain0
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Comment: C: unable to load xps
... Hi Christian, I am now able to install xps from the source code (not from the tar file from bioconductor as it is not from the latest version). But for some reason, the package is still not loading on RStudio but is loading without any error from R terminal. Thank you for all your support! Regard ...
written 10 months ago by Ashish Jain0
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Comment: C: unable to load xps
... Hi Christian, It seems that DYLD_LIBRARY_PATH and LD_LIBRARY_PATH are required by xps (in Redhat also) as I was not able to install the package without these paths (As xps is not able to locate libClint.so file which is in lib folder of root). For a quick fix can you please point me to the files in ...
written 10 months ago by Ashish Jain0
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Comment: C: unable to load xps
... - I am able to run the 'demos.C' from the directory root/tutorials. - My '.bashrc' file is: # .bashrc # Source global definitions if [ -f /etc/bashrc ]; then         . /etc/bashrc fi # Uncomment the following line if you don't like systemctl's auto-paging feature: # export SYSTEMD_PAGER= # User ...
written 11 months ago by Ashish Jain0
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Comment: C: unable to load xps
... And one more thing, I am able to install the package from the command line (from source) but I was not able to load it. Error while loading: Error: package or namespace load failed for ‘xps’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/home/jain/R/x86_64-redhat-linux ...
written 11 months ago by Ashish Jain0
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Comment: C: unable to load xps
... Hi Christian, Thank you for the reply. Please find my answers below: - Did you download ROOT from: https://root.cern.ch/content/release-53436 Yes, I downloaded ROOT from this link. - Did you download and compile the source code yourself?   (This is the option I recommend) I did complied the sou ...
written 11 months ago by Ashish Jain0
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Comment: C: unable to load xps
... Also, when I am trying to install it from RStudio via Bioconductor it is giving me error that ROOTSYS variable is not there. > biocLite("xps",type="source") BioC_mirror: https://bioconductor.org Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23). Installing package(s) ‘xps’ try ...
written 11 months ago by Ashish Jain0

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