User: Chirag Parsania
Chirag Parsania • 930
- Reputation:
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- University of Macau
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Posts by Chirag Parsania
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... 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 Parsania • 930
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... 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 Parsania • 930
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... 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 Parsania • 930
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... 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 ...
written 7 weeks ago by
Chirag Parsania • 930
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... 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 ...
written 7 weeks ago by
Chirag Parsania • 930
• updated
6 weeks ago by
zx8754 ♦ 4.8k
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... 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 Parsania • 930
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... 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 Parsania • 930
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... [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 Parsania • 930
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... [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 Parsania • 930
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... 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 Parsania • 930
Latest awards to Chirag Parsania
Popular Question
25 days ago,
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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?
Student
10 weeks ago,
asked a question with at least 3 up-votes.
For For a given set of NCBI taxonomy ids / species names, how to derive their species to species distance matrix ?
Scholar
11 weeks ago,
created an answer that has been accepted.
For A: GO enrichment - interpreting broad terms
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For C: Reorder heatmap rows in a dataset with missing values
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For C: Reorder heatmap rows in a dataset with missing values
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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
Appreciated
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For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
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created 100 posts.
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For A: GO enrichment - interpreting broad terms
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For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
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For Z-Score calculation by heatmap.2
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For Extract reads from bam/sam files using read id
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11 months ago,
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For How to find intron co-ordinates from the gff file?
Scholar
12 months ago,
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For A: GO enrichment - interpreting broad terms
Scholar
13 months ago,
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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
Appreciated
20 months ago,
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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
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2.0 years ago,
created a question with more than 1,000 views.
For Z-Score calculation by heatmap.2
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