User: Chirag Parsania

gravatar for Chirag Parsania
Reputation:
930
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Trusted
Location:
University of Macau
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Google Scholar Page
Last seen:
3 days, 20 hours ago
Joined:
3 years, 1 month ago
Email:
c**************@gmail.com

Posts by Chirag Parsania

<prev • 128 results • page 1 of 13 • next >
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Comment: C: FASTA file with taxid, want to obtain lineage and put into header
... First you have to convert accession to NCBI tax id then you can get full lineage using following R function #' Title #' #' @param ncbi_tax_ids : a vector of NCBI tax_ids #' @param ncbi_tax_dir : directory having ncbi tax files #' #' @return : a tibble having tax_id plus al ...
written 18 days ago by Chirag Parsania930
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Comment: C: How does ggtree interprets branch support value (e.g bootstrap value) given as n
... Hi Guangchuang, Thanks for your reply. I didn't realise that `root` belongs `ape`. Anyway, I checked the documentation of `ape::root.` Infect after the [critical review][1] rerooting function of `ape` have been updated. [1]: https://academic.oup.com/mbe/article/34/6/1535/3077051 ...
written 6 weeks ago by Chirag Parsania930
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Comment: C: Pairwise distance of rooted phylogenetic tree
... Hi thanks for reply. I am trying to compare species tree vs gene tree. However, I have 100s of horizontally transferred (HT) genes an therefore it is not practical to make pair of species tree and gene tree for each of them and then compare with gene tree. To address this, I designed alternate anal ...
written 7 weeks ago by Chirag Parsania930
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Pairwise distance of rooted phylogenetic tree
... Hi, I am quite new to phylogenetic analysis. Please bare with me if question does not make sense. I am using IQtree to analyse some horizontally transferred genes. I have successfully generated phylogenetic tree using IQtree. I have few questions related to interpretation of the trees given by ...
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How does ggtree interprets branch support value (e.g bootstrap value) given as node label?
... Hi, I came [across the paper][1] describing issues interpreting phylogenetic tree due to branch support given as node label in newick format. Let me describe the problem very briefly, which is explained in depth in the paper given above. Many tree output programmes gives branch support values (e ...
phylogenetic R ggtree newick written 7 weeks ago by Chirag Parsania930 • updated 6 weeks ago by zx87544.8k
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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 10 weeks ago by Chirag Parsania930
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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 11 weeks ago by Chirag Parsania930
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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 11 weeks ago by Chirag Parsania930
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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 11 weeks ago by Chirag Parsania930
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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 11 weeks ago by Chirag Parsania930

Latest awards to Chirag Parsania

Popular Question 25 days ago, created a question with more than 1,000 views. For Cross correlation analysis in R
Student 6 weeks ago, asked a question with at least 3 up-votes. For How to find intron co-ordinates from the gff file?
Scholar 11 weeks ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: Reorder heatmap rows in a dataset with missing values
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: Reorder heatmap rows in a dataset with missing values
Good Answer 12 weeks 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 12 weeks ago, created 100 posts.
Scholar 12 weeks ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Teacher 12 weeks 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 3 months ago, created a question with more than 5,000 views. For Z-Score calculation by heatmap.2
Popular Question 9 months ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Student 11 months ago, asked a question with at least 3 up-votes. For How to find intron co-ordinates from the gff file?
Scholar 12 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Scholar 13 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Popular Question 13 months ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Scholar 13 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Popular Question 14 months ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Good Answer 20 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 20 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 2.0 years ago, created a question with more than 1,000 views. For Z-Score calculation by heatmap.2

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