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User: Chirag Parsania

gravatar for Chirag Parsania
Chirag Parsania • 1.2k
Reputation:
1,210
Status:
Trusted
Location:
University of Macau
Scholar ID:
Google Scholar Page
Last seen:
5 days, 12 hours ago
Joined:
3 years, 5 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 • 162 results • page 1 of 17 • next >
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Comment: C: shinyChromosome: an R/Shiny application for interactive creation of non-circular
... Hi, is the paper out for shinyChromosome ? ...
written 17 days ago by Chirag Parsania • 1.2k
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Answer: A: K-means With Many Clusters: Quick-TRANSfer steps exceeded
... Hi, You can try one of the recently published clustering method "Clust". Here is the [paper][1] . In this method, user do not need to define number of clusters. Method itself detects number of clusters and also removes observations which does not contribute to the variability across the samples. Me ...
written 28 days ago by Chirag Parsania • 1.2k
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Comment: C: How to plot a profile showing read coverage around the 5 prime splice site?
... I would suggests, to take all the isoforms for a given gene. The reason for that is, anyway you want to look at the overall profile between the conditions. If there is any differences, it will be shown up. However, if you want to do the same analysis at gene level, then you can think of considering ...
written 6 weeks ago by Chirag Parsania • 1.2k
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Comment: C: How to plot a profile showing read coverage around the 5 prime splice site?
... One way to do this is, get all the transcripts (CDS) co-ordinates from the gff file. Once you have CDS co-ordinates, align them by 5' region and define flanking bp (eg +/- 500 bp) and write them into bed file. ...
written 6 weeks ago by Chirag Parsania • 1.2k
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Comment: C: Correlation between lncRNA and protein coding genes
... Short description. if you have a pair of a variable (X and Y) then value `R^2` and `r^2 (output of cor)` is the same. However, power of R^2 comes into the picture in multiple linear regression problem where multiple variables simultaneously used to predict the response. Reference : Excerpt Fro ...
written 7 weeks ago by Chirag Parsania • 1.2k
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Comment: C: plot phylogenetic tree with ggtree
... Can you upload your tree and matrix data ? ...
written 7 weeks ago by Chirag Parsania • 1.2k
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Comment: C: How to tidy data with more-than one header, while both headers in long format
... Hi cpad0112, don't you think using `sapply` , subsetting by `[]` and `str_split_fixed` makes less readable compare to using `tidyverse` verbs `slice`, `summarise_all` and `separate`. Just a thought. Nothing personal :) ...
written 7 weeks ago by Chirag Parsania • 1.2k
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Answer: A: How to tidy data with more-than one header, while both headers in long format
... See below if it make sense. d <- inputdata ## extract headers headers <-d %>% dplyr::slice(c(1:2)) ## extract data data <- d %>% dplyr::slice(-c(1:2)) %>% mutate_all(as.numeric) ## make header in to one row headers <- headers ...
written 7 weeks ago by Chirag Parsania • 1.2k
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Comment: C: standalone blast output to excel
... >which needs to have only aligned sequence the corresponding sequence id. Could you please explain more ? ...
written 7 weeks ago by Chirag Parsania • 1.2k
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Comment: C: R bioconductor package `rtracklayer` possible memory leakage
... Sorry. !! Now it appears there. GitHub behaving weirdly. See the link in above comment. ...
written 8 weeks ago by Chirag Parsania • 1.2k

Latest awards to Chirag Parsania

Scholar 7 weeks ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Teacher 7 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
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Scholar 8 weeks ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Scholar 8 weeks ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Teacher 8 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
Guru 8 weeks ago, received more than 100 upvotes.
Supporter 8 weeks ago, voted at least 25 times.
Teacher 8 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
Teacher 8 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
Autobiographer 8 weeks ago, has more than 80 characters in the information field of the user's profile.
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
Popular Question 4 months ago, created a question with more than 1,000 views. For Cross correlation analysis in R
Popular Question 4 months ago, created a question with more than 1,000 views. For Cross correlation analysis in R
Student 5 months ago, asked a question with at least 3 up-votes. For How to find intron co-ordinates from the gff file?
Student 6 months 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 6 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Reorder heatmap rows in a dataset with missing values
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Reorder heatmap rows in a dataset with missing values
Good Answer 6 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 6 months ago, created a post with more than 5 votes. For A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
Centurion 6 months ago, created 100 posts.
Scholar 6 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Teacher 6 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 7 months ago, created a question with more than 5,000 views. For Z-Score calculation by heatmap.2
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