User: Prakash

gravatar for Prakash
Prakash2.0k
Reputation:
2,030
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Location:
India
Twitter:
gprakash047
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Last seen:
1 day, 10 hours ago
Joined:
5 years, 2 months ago
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Posts by Prakash

<prev • 151 results • page 1 of 16 • next >
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Answer: A: Quantification of acetylation enriched regions at transcription factor binding s
... One suggestion would be to quantify the H3K27ac enrichment ± 5kb (or ± 2kb) relative to peak summit for the given set of identified TF binding sites of your interest. This can be performed in HOMER using option `e.g -size 5000 -hist 10` . More detail can be found [here][1] . Further graphically it ...
written 15 days ago by Prakash2.0k
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Answer: A: WGCNA "trait" file format?
... ploting heatmap using complexheatmap alternative to `labeledHeatmap` # Define numbers of genes and samples nGenes = ncol(datExpr); nSamples = nrow(datExpr); # Recalculate MEs with color labels MEs0 = moduleEigengenes(datExpr, dynamicColors)$eigengenes MEs = orderMEs(MEs0) ...
written 19 days ago by Prakash2.0k
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Comment: C: Dividing the groups on the same axis using ggplot2
... I think it is showing the error because you have mentioned "Groups" instead of "Group" for x axis. ggplot(data, aes(x=Group, y=Pathway, size=DEGs, color=Padj)) + geom_point(alpha = 0.8) + facet_wrap(Group ~ .) + theme_classic() ...
written 7 weeks ago by Prakash2.0k
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Comment: C: BWA mem and Samtools sort in Bash script
... Thanks [WoterDeCoster][1] for this information [1]: https://www.biostars.org/u/24526/ ...
written 3 months ago by Prakash2.0k
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Comment: A: BWA mem and Samtools sort in Bash script
... I think you need to also add `-O BAM` argument to write the output to file ...
written 3 months ago by Prakash2.0k
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Comment: C: Unable to locate libraries in latest version of R 4.0.0
... Recently I had similar issue, then I had to recompile everything. I just took the list of packages from the existing library. Here you can use your own library path pkgs <- rownames(installed.packages(lib.loc = "/Users/mtoufiq/Library/R/3.5/library")) and compile everything as suggested by ...
written 4 months ago by Prakash2.0k
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Answer: A: GoProfiler compareGeneLists Error
... I tried to reproduce your problem, however, in my case, I didn' get the error that you encountered. Here is the output that I got > print(gene1Compared) $MF linear combination of chi-squares statistic data: expanded1[[i]] and expanded2[[i]] and NULL (n*m/(n+m)) * ...
written 5 months ago by Prakash2.0k
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Comment: C: error in reorder the bars of ggplots
... x =reorder(Term, -logPValue) should work ...
written 5 months ago by Prakash2.0k
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Comment: C: Changing distance to TSS (tssRegion in ChIPseeker) during peak annotation in ChI
... The basic principle for ChIP-seq peaks annotation is to identify the nearest TSS (genes). so even though you increase the range of window upstream or downstream of TSS the number of annotated genes will remain constant. But In case you increase it to 10000, one peak might be annotated to several ge ...
written 5 months ago by Prakash2.0k
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Comment: C: GSEA/fold change for ChIP-seq
... Apart from peak calling and annotation, ChIPseq data can also be used to find differential genomic regions across conditions. [DiffBind][1] performs such kind of analysis that internally uses [DESeq2][2] for differential analysis. Similar to raw count for genes, Diffbind extracts raw counts for geno ...
written 6 months ago by Prakash2.0k

Latest awards to Prakash

Teacher 5 days ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Good Answer 29 days ago, created an answer that was upvoted at least 5 times. For A: How to add gene symbol to RNA-Seq data using R
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Popular Question 5 months ago, created a question with more than 1,000 views. For Error while running computeMatrix of deepTools
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Voter 7 months ago, voted more than 100 times.
Student 8 months ago, asked a question with at least 3 up-votes. For Motif analysis from H3K27ac ChIPseq broad peaks
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Delete numbers in the tables column
Appreciated 13 months ago, created a post with more than 5 votes. For A: How to add colors to bar chart?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Popular Question 13 months ago, created a question with more than 1,000 views. For Error while running computeMatrix of deepTools
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Appreciated 14 months ago, created a post with more than 5 votes. For A: How to add colors to bar chart?
Appreciated 14 months ago, created a post with more than 5 votes. For A: Delete numbers in the tables column
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: How to add gene symbol to RNA-Seq data using R
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: How to add gene symbol to RNA-Seq data using R
Appreciated 15 months ago, created a post with more than 5 votes. For A: How to add colors to bar chart?
Appreciated 15 months ago, created a post with more than 5 votes. For A: How to add colors to bar chart?
Scholar 15 months ago, created an answer that has been accepted. For A: How to add colors to bar chart?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Scholar 15 months ago, created an answer that has been accepted. For A: How to add colors to bar chart?

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