User: Chirag Parsania

gravatar for Chirag Parsania
Chirag Parsania1.8k
Reputation:
1,840
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Location:
University of Macau
Scholar ID:
Google Scholar Page
Last seen:
3 days, 9 hours ago
Joined:
4 years, 11 months ago
Email:
c**************@gmail.com

All answered queries can also be found on github https://github.com/cparsania/biostar_queries

 

 

Posts by Chirag Parsania

<prev • 218 results • page 2 of 22 • next >
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Comment: C: How to get the response variable from gbm model when train.fraction is <1 ?
... 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 9 weeks ago by Chirag Parsania1.8k
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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 9 weeks ago by Chirag Parsania1.8k
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Comment: C: How to check quality of multiple sequence alignment (MSA)?
... Hi, Thanks for reply. I updated original question. Kindly check. ...
written 11 weeks ago by Chirag Parsania1.8k
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How to check quality of multiple sequence alignment (MSA)?
... 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, ...
R multiple sequence alignment msa written 11 weeks ago by Chirag Parsania1.8k
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Comment: C: How to check for the presence/absence of unique rows in two different matrices?
... `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 3 months ago by Chirag Parsania1.8k
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Answer: A: How to get Taxonomy and Taxon ID for an Accession number using R/Python?
... 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 3 months ago by Chirag Parsania1.8k
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Comment: C: MrBayes: Implementing the LG model
... 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 4 months ago by Chirag Parsania1.8k
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Answer: A: Obtaining nucleotide sequences from a set of protein identifiers
... 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 6 months ago by Chirag Parsania1.8k
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Comment: C: Plotting a line graph using the ggplot2 for multiple columns (genes)
... 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 6 months ago by Chirag Parsania1.8k
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Comment: C: Plotting a line graph using the ggplot2 for multiple columns (genes)
... Explained in [this post][1]. Kindly refer. [1]: https://www.biostars.org/p/343055/#343604 ...
written 6 months ago by Chirag Parsania1.8k

Latest awards to Chirag Parsania

Scholar 4 weeks ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Teacher 5 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
Scholar 5 weeks ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Great Question 6 weeks ago, created a question with more than 5,000 views. For Extract reads from bam/sam files using read id
Popular Question 5 months ago, created a question with more than 1,000 views. For Why cufflink gives two transcripts/isoforms for one particular ORF ??
Scholar 7 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Teacher 7 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
Teacher 7 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
Teacher 8 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
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How can I separate column names in to different columns to perform downstream an
Good Question 8 months ago, asked a question that was upvoted at least 5 times. For How to find intron co-ordinates from the gff file?
Teacher 9 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
Scholar 9 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Teacher 10 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
Epic Question 11 months ago, created a question with more than 10,000 views. For Z-Score calculation by heatmap.2
Popular Question 11 months ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Popular Question 13 months ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Popular Question 15 months ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Scholar 15 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Scholar 16 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Teacher 16 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
Scholar 16 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms

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