User: Chirag Parsania

gravatar for Chirag Parsania
Reputation:
890
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Trusted
Location:
University of Macau
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Google Scholar Page
Last seen:
1 day, 8 hours ago
Joined:
2 years, 11 months ago
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c**************@gmail.com

Posts by Chirag Parsania

<prev • 123 results • page 1 of 13 • next >
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Comment: C: Plotting traits on phylogenetic tree in R - issue with aligning traits
... I am not expert of phytools. But I love using [ggtree][1]. Worth trying this for tree visualisation in R [1]: https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtree.html ...
written 13 days ago by Chirag Parsania890
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Comment: C: Common Newick Trees with "proximities" for use with PhyloGibbs
... A tree showing universal relation between species can be downloaded from NCBI taxonomy database using common tree functionality. In that, for given taxonomical ids you can download species tree in newick format. For more details about tree download and loading in the R [follow this thread.][1] ...
written 19 days ago by Chirag Parsania890
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Comment: C: database for searching introns or exons which contain known binding site
... [JASPAR][1] is the way to go. It gives you the list of binding sites with chromosomal locations in fasta format. Couldn't find FOX1 but [FOXA1 is there.][2] [1]: http://jaspar.genereg.net [2]: http://jaspar.genereg.net/matrix/MA0148.1/ ...
written 19 days ago by Chirag Parsania890
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Comment: C: plotting the expression profiles of different conditions in same plot
... [ComplexHeatmap][1] might help. [1]: https://bioconductor.org/packages/release/bioc/vignettes/ComplexHeatmap/inst/doc/s4.heatmap_annotation.html ...
written 19 days ago by Chirag Parsania890
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Answer: A: How to plot heatmap for the matrix for the pairwise comparison of sequence simi
... You can use `corrplot` from package `corrplot` to generate the matrix heatmap. You can use your Table 2 as input. However, it will show you one of the half of given matrix. `as.matrix` should work to convert Table 1 to Table 2 corrplot::corrplot(as.matrix(dd) , is.corr = FALSE , type = "upper ...
written 22 days ago by Chirag Parsania890
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Comment: C: Extracting certain columns from VCF file
... if you want GUI based program [this is the one to use][1] [1]: https://biomedical-sequencing.at/VCFFilter/ ...
written 23 days ago by Chirag Parsania890
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Comment: C: Get non redundant from Bacteria Archaea Fungi
... Hi, get NCBI taxonomy id for each downloaded protein. Assign kingdom (Bacteria, Archea , Plant, Fungi , Matazoa etc) using taxonomy id. ([Follow this thread][1] to map kingdom information to taxid). [1]: https://www.biostars.org/p/317073/#317239 ...
written 23 days ago by Chirag Parsania890
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Comment: C: Filtering a list of protein sequences with no homolog in bacteria
... orthodb might helps here. It gives list of genes with their orthologous groups. You can filter out genes which do not have orthologous in bacteria. Ortho db data can be downloaded from [here][1]. [1]: http://www.orthodb.org/?page=downloads ...
written 23 days ago by Chirag Parsania890
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Comment: C: FASTA file with taxid, want to obtain lineage and put into header
... Hi Chris, Good to know this `rankedlineage.dmp`. It must be much faster than what I suggested. ...
written 23 days ago by Chirag Parsania890
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Answer: A: FASTA file with taxid, want to obtain lineage and put into header
... Here, I assume that you know bit of R programming and you can tweak R functions. I wrote a `R function` to get NCBI kingdom names from ncbi taxonomy id. You can modify function to get various level of taxonomy and then create your own fasta header. In the given function below, you can define t ...
written 25 days ago by Chirag Parsania890

Latest awards to Chirag Parsania

Scholar 20 days ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Commentator 20 days ago, created a comment with at least 3 up-votes. For C: Reorder heatmap rows in a dataset with missing values
Commentator 23 days ago, created a comment with at least 3 up-votes. For C: Reorder heatmap rows in a dataset with missing values
Good Answer 27 days ago, created an answer that was upvoted at least 5 times. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Centurion 28 days ago, created 100 posts.
Scholar 28 days ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Great Question 6 weeks ago, created a question with more than 5,000 views. For Z-Score calculation by heatmap.2
Popular Question 7 months ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Student 9 months ago, asked a question with at least 3 up-votes. For How to find intron co-ordinates from the gff file?
Scholar 10 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Scholar 11 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Popular Question 11 months ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Scholar 11 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Popular Question 12 months ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Popular Question 22 months ago, created a question with more than 1,000 views. For Z-Score calculation by heatmap.2

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