User: Chirag Parsania

gravatar for Chirag Parsania
Reputation:
990
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Trusted
Location:
University of Macau
Scholar ID:
Google Scholar Page
Last seen:
6 hours ago
Joined:
3 years, 3 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 • 134 results • page 1 of 14 • next >
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Comment: C: [Crushing the bureaucracy in bioinformatics] Introducing Skymap-JupyterHub: acce
... I wonder what organisms will be covered in the project ? As of now I can see Canis familiaris, Danio rerio ,Drosophila, Human and Mouse for RNAseq data. Should I expect any update in the organism list in the future ? ...
written 20 hours ago by Chirag Parsania990
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Comment: C: Unsupervised selection of inter-cluster highly variable genes
... easiest way is to calculate the stndard deviation for each gene across the samples in each cluster. Once you get SD value, rank each cluster by SD from high to low and then select top genes from each cluster. This will give you highly variable genes across the samples within each cluster and probabl ...
written 21 hours ago by Chirag Parsania990
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Answer: A: Compare data from two different table using R
... Here is the dplyr way. Make sure that you provide column names as given in `t1` and `t2` library(tidyverse) t1 <- tibble(X1 = c("a;b","c","d;e")) t2 <- tibble(Y1 =letters[1:5] , Y2 = c("uuu","vvv","xxx","yyy","zzz") ,Y3 =c("uu","vv","xx","yy","zz")) ...
written 21 hours ago by Chirag Parsania990
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Comment: C: How to make k-means clustering plot for relative expression?
... Hi Prakash, as of now I don't have any systematic way to do that. But I use crude way to decide number of K. For example, I check visually (using heatmap or lineplot shown above) if observations in particular cluster behaves similarly. If not, I keep on changing K value till I get convincing cluster ...
written 1 day ago by Chirag Parsania990
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Answer: A: How to make cluster from gene read count?
... Hi, First you can find the top genes which are highly variable across the conditions. One way to do this is calculate the standard deviation (SD) across the sample for each gene and then arrange from high to low using SD values. You can choose top 10% or 20% of the genes and later parform k-means on ...
written 1 day ago by Chirag Parsania990
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Answer: A: How to make k-means clustering plot for relative expression?
... Hi, here is the solution using dplyr. In the script below, you need to set the path of tab delim .txt file at `file_path` variable. In the given files, columns should be variables and rows should be observations (E.g. genes). Each column and row must have unique identity given as first row and firs ...
written 1 day ago by Chirag Parsania990
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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 10 weeks ago by Chirag Parsania990
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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 3 months ago by Chirag Parsania990
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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 3 months ago by Chirag Parsania990
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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 ...

Latest awards to Chirag Parsania

Teacher 1 day 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
Autobiographer 1 day ago, has more than 80 characters in the information field of the user's profile.
Teacher 23 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
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Cross correlation analysis in R
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Cross correlation analysis in R
Student 3 months ago, asked a question with at least 3 up-votes. For How to find intron co-ordinates from the gff file?
Scholar 4 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Reorder heatmap rows in a dataset with missing values
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Reorder heatmap rows in a dataset with missing values
Good Answer 4 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
Centurion 4 months ago, created 100 posts.
Scholar 4 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Teacher 4 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
Great Question 5 months ago, created a question with more than 5,000 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
Student 13 months ago, asked a question with at least 3 up-votes. For How to find intron co-ordinates from the gff file?
Scholar 14 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Scholar 15 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
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
Popular Question 16 months ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Good Answer 22 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

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