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User: Chirag Parsania

gravatar for Chirag Parsania
Chirag Parsania • 1.7k
Reputation:
1,720
Status:
Trusted
Location:
University of Macau
Scholar ID:
Google Scholar Page
Last seen:
5 days, 5 hours ago
Joined:
4 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 • 201 results • page 1 of 21 • next >
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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 14 days ago by Chirag Parsania • 1.7k
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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 15 days ago by Chirag Parsania • 1.7k
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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 16 days ago by Chirag Parsania • 1.7k
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Answer: A: Extract sequences consecutively from a large fasta files and save in new fasta f
... **R way** sp1_fa <- Biostrings::readBStringSet("species1.fasta") sp2_fa <- Biostrings::readBStringSet("species2.fasta") purrr::map(seq_along(sp1_fa) , ~ Biostrings::writeXStringSet( filepath = paste("group" ,..1,".fasta",sep = "") , ...
written 26 days ago by Chirag Parsania • 1.7k
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Comment: C: Mapping common identifiers between two files
... Have a look into `dplyr` joins. `dplyr::left_join(df1, df2)` keep all the rows from `df1`. `dplyr::right_join(df1, df2)` keep all the rows from `df2`. ...
written 4 weeks ago by Chirag Parsania • 1.7k
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Answer: C: Could you please explain Fold change, % of change, and log2 fold change (L2FC) t
... All the figures you posted above shows same thing which is Log2(FoldChange). Although 1st figure x axis labeled "Fold Change" it is Log2(FoldChange). Without log you cannot have negative values (It means down regulated genes). One of the reasons to use log2(FoldChange) and not FoldChange only is t ...
written 5 weeks ago by Chirag Parsania • 1.7k
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Answer: C: ggplot density plot across bed file
... Replace `mpg` to your `data.frame` and `cty` to ` V4` library(tidyverse) mpg %>% ggplot() + geom_density(aes(x = cty)) ![](https://i.imgur.com/58yDF5H.png) ...
written 10 weeks ago by Chirag Parsania • 1.7k • updated 10 weeks ago by zx8754 ♦ 8.7k
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Comment: C: Get cDNA sequences from NCBI for given protein IDs
... I wrote complete solution [here][1] in step by step manner [1]: http://rpubs.com/parsaniac/ncbi_protein_id_to_cds ...
written 3 months ago by Chirag Parsania • 1.7k
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Comment: C: GO analysis to ID biological processes in my identified protein list? panther? a
... [ClusterProfiler][1] is one of my favourite. [1]: https://yulab-smu.github.io/clusterProfiler-book/chapter1.html ...
written 3 months ago by Chirag Parsania • 1.7k
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Comment: C: Metabolic pathway Mapping
... One way to map KEGG pathway is using [KEGG mapper][1] [1]: https://www.genome.jp/kegg/tool/map_pathway2.html ...
written 3 months ago by Chirag Parsania • 1.7k

Latest awards to Chirag Parsania

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
Teacher 6 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 10 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 10 weeks 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 3 months ago, asked a question that was upvoted at least 5 times. 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
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
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
Epic Question 5 months ago, created a question with more than 10,000 views. For Z-Score calculation by heatmap.2
Popular Question 6 months ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Popular Question 7 months ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Popular Question 9 months ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Appreciated 9 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
Scholar 9 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Scholar 10 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Appreciated 11 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
Scholar 11 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Teacher 11 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 13 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 13 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Appreciated 13 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
Scholar 13 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Teacher 13 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 13 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
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