User: Prakash

gravatar for Prakash
Prakash2.1k
Reputation:
2,060
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Location:
India
Twitter:
gprakash047
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Last seen:
4 hours ago
Joined:
5 years, 5 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 3 months ago by Prakash2.1k
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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 3 months ago by Prakash2.1k
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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 4 months ago by Prakash2.1k
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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 5 months ago by Prakash2.1k
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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 5 months ago by Prakash2.1k
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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 7 months ago by Prakash2.1k
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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 7 months ago by Prakash2.1k
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Comment: C: error in reorder the bars of ggplots
... x =reorder(Term, -logPValue) should work ...
written 8 months ago by Prakash2.1k
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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 8 months ago by Prakash2.1k
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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 9 months ago by Prakash2.1k

Latest awards to Prakash

Popular Question 6 weeks ago, created a question with more than 1,000 views. For Error while running computeMatrix of deepTools
Great Question 8 weeks ago, created a question with more than 5,000 views. For Complexheatmap annotation legend
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Error while running computeMatrix of deepTools
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Good Answer 3 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
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Popular Question 7 months ago, created a question with more than 1,000 views. For Error while running computeMatrix of deepTools
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Voter 9 months ago, voted more than 100 times.
Student 11 months ago, asked a question with at least 3 up-votes. For Motif analysis from H3K27ac ChIPseq broad peaks
Teacher 11 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?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Delete numbers in the tables column
Teacher 15 months ago, created an answer with at least 3 up-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?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Popular Question 16 months ago, created a question with more than 1,000 views. For Error while running computeMatrix of deepTools
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Good Answer 16 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 16 months ago, created a post with more than 5 votes. For A: Delete numbers in the tables column
Appreciated 16 months ago, created a post with more than 5 votes. For A: How to add colors to bar chart?
Good Answer 17 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 17 months ago, created a post with more than 5 votes. For A: How to add colors to bar chart?
Appreciated 18 months ago, created a post with more than 5 votes. For A: How to add colors to bar chart?

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