User: Chirag Parsania
Chirag Parsania • 1.7k
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Posts by Chirag Parsania
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Comment:
C: FASTA file split
... try command faSplit given by [UCSC utilities][1].
[1]: http://hgdownload.soe.ucsc.edu/admin/exe/ ...
written 2 days ago by
Chirag Parsania • 1.7k
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... If possible provide minimum reproducible example. I would suggest you to explore R tidyModels. Probably function `broom::tidy()` could solve your problem. See the example below where I used model created by `lm()` function and later get model details using `broom::tidy()`
library(tidyverse) ...
written 6 days ago by
Chirag Parsania • 1.7k
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Comment:
C: NGSseq heatmap RStudio
... Try [ComplexHeatmap][1] R package. It internally handles clustering stuff. You just need to give your expression matrix.
[1]: https://jokergoo.github.io/ComplexHeatmap-reference/book/ ...
written 6 days ago by
Chirag Parsania • 1.7k
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... Hi, Thanks for reply. I updated original question. Kindly check. ...
written 22 days ago by
Chirag Parsania • 1.7k
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... tl;dr; I wonder , is there any known tool / webserver / r package to check quality of MSA ?
---- EDIT -----
The idea here is, for a given protein sequence to find out set of orthologues and perform the phylogenetic analysis. To do so, I performed blast and got first set of orthologues. However, ...
written 23 days ago by
Chirag Parsania • 1.7k
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... `dplyr::left_join(matrix1 , matrix2 ,by = "common_column_to_be_used_to_join_two_matrix" )` will give all the rows from matrix1 and all the columns from matrix2.
PS : First you need to convert matrix in to `dataframe` or `tibble` objects.
========== EDIT==========
library(dplyr)
#>
...
written 6 weeks ago by
Chirag Parsania • 1.7k
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... I have been writing an R package to deal with taxonomy mapping for blast outcome. The package is in very initial stage. However, there are functions which can solve your problem. You can install package using `devtools::install_github("cparsania/phyloR")`.
See the example below
library(p ...
written 7 weeks ago by
Chirag Parsania • 1.7k
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... Hi, Can I use FreeRate model as given here in IQTREE (http://www.iqtree.org/doc/Substitution-Models). I ran the IQTREE to generate the MaximumLikelihood tree. For the given dataset, IQTREE ran ModelFinder to choose best model to my data, which is LG+R6. Now I want to generate Bayesian tree using Mr ...
written 12 weeks ago by
Chirag Parsania • 1.7k
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... Check [this out][1]. Step by step guidance to obtain CDS from protein ID. It may help.
[1]: http://rpubs.com/parsaniac/ncbi_protein_id_to_cds ...
written 4 months ago by
Chirag Parsania • 1.7k
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... In the plot above you showed, you should make `value` column to `numeric` rather `character`. It will make your y-axis visually look much better than current. Also, if you have more than 100 genes to show each with name of each in legend, probably line plot is not a good idea. Better you use heatma ...
written 4 months ago by
Chirag Parsania • 1.7k
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For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
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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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17 months ago,
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For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
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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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17 months ago,
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For A: GO enrichment - interpreting broad terms
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