User: ####

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####90
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Bioinformatician, proficient in handling NGS & Micro-array data.
 

Posts by ####

<prev • 87 results • page 1 of 9 • next >
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Answer: A: ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualiz
... Hi thanks for your reply, clusterProfiler is not getting updated I have updated my R version to 3.4 and then installed ReactomePA & Clusterprofiler but I am getting the same old version of both the packages. Can anyone you now tell me what could be the solution for this? Here is the output of m ...
written 4 days ago by ####90
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Answer: A: ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualiz
... I am using ReactomePA and my input looks like this,entrezId & p-value : > gene 433016 16365 16891 71816 170835 71738 100034251 14058 215257 245126 108078 20558 57248 16456 56619 17474 20288 64292 14727 71519 ...
written 5 days ago by ####90
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Ensembl Biomart Plant database
... I want to fetch Arabidospsis annotation via ensembl biomart R package, here is the example how I am trying to fetch it: library("biomaRt") species = athaliana db = useMart(biomart = "plants_mart",paste(species,"_eg_gene",sep=""), host = "plants.ensembl.org") features = ...
R bioconductor biomart written 5 weeks ago by ####90 • updated 5 weeks ago by Mike Smith200
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Comment: C: GTF/GFF file for feature count
... Devon Thanks, along with " there was a wide space as well after removing both it worked.Thanks ...
written 10 weeks ago by ####90
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Comment: C: GTF/GFF file for feature count
... I am aware about these two options you have mentioned, I have edited the gtf file mentioned above, I am getting following warning while running featureCounts with no output file: Warning: failed to find the gene identifier attribute in the 9th column of the provided GTF file. The specified ...
written 11 weeks ago by ####90
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Comment: C: DESeq2 for non-model organisms
... I hope you can ignore un-organized way of posting... So I do and I have used featureCounts as well. My point is not generating matrix so my point is to use non-model organism for RNA-seq analysis using DESeq2 and as you know DESeq2 has a BiomaRt r package , which can help user to use particular org ...
written 11 weeks ago by ####90
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Answer: A: DESeq2 for non-model organisms
... Cannot generate that. Was looking for a way to call genome via Biomart as the genome is there in Ensembl but from `listDatasets(ensembl)` in `R` cannot see or find that organism. ...
written 11 weeks ago by ####90
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DESeq2 for non-model organisms
... I want to perform RNA-Seq analysis on non-model organism data using `DESeq2` , as its well known that DESeq2 uses `Biomart` for organism references like : `hsapiens or mmusculus for human or mouse` My organism is non-model and I am trying to find out option/s to do so. Any inputs on this...?? Tha ...
deseq2 rna-seq written 11 weeks ago by ####90
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Comment: C: fasta seq header
... In this case if instead of printing 1st I tried to print lets say 4th id after the pipe : cat gene.fasta | paste - - |awk '{ split($1,a,"|");print a[4] "\n" $2}' its just printing the id and not the sequences ...
written 12 weeks ago by ####90
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Comment: C: fasta seq header
... No in this case I want first id ..i.e. gene_1 ...
written 12 weeks ago by ####90

Latest awards to ####

Scholar 5 months ago, created an answer that has been accepted. For A: IGV custom Genome
Autobiographer 5 months ago, has more than 80 characters in the information field of the user's profile.
Supporter 13 months ago, voted at least 25 times.

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