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User: Chirag Parsania

gravatar for Chirag Parsania
Chirag Parsania • 1.4k
Reputation:
1,410
Status:
Trusted
Location:
University of Macau
Scholar ID:
Google Scholar Page
Last seen:
3 days, 15 hours ago
Joined:
3 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 • 174 results • page 1 of 18 • next >
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Comment: C: How to extract a entire row based on a single key word from a csv or excel file?
... Don't understand this part. > For example the avrbs2 and avrbs3 repeated over 50 to 60 times in the excel/csv sheet, from that I need to extract the same without redundancy. Do you mean you want to extract first occurrence only ? Can you put sample input and sample output ? ...
written 3 months ago by Chirag Parsania • 1.4k
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Blog: Bioinformatics perspective from senior scientist.
... Hi, I came across one of the recent interview of very senior bioinformatician **Professor G.P.S Raghava** [(**> 12k citations on google scholar**)][1]. I feel his thoughts on bioinformatics will help young researcher (specially PhD students) to reshape their thinking. In his interview, he touched ...
bioinformatics blog interview written 3 months ago by Chirag Parsania • 1.4k
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Comment: C: How to create a summary statistics data table for omics data?
... Check my updates in the answer. ...
written 3 months ago by Chirag Parsania • 1.4k
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Comment: C: How to create a summary statistics data table for omics data?
... I'm sure you will be able to explore from the code I posted. For more reference regarding to pvalue, error bar and other statistics refere [this][1]. [1]: https://i.ibb.co/Fn8NPh9/boxplot.png ...
written 3 months ago by Chirag Parsania • 1.4k • updated 3 months ago by genomax ♦ 68k
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Answer: A: How to create a summary statistics data table for omics data?
... I showed few tactics to simplify and visualise data in R using `tidyverse` You can explore more by taking this as start point. library(tidyverse) ss <- df %>% as_tibble() %>% gather(key = "cond" , value = "value" , -AGI) %>% ## wide to long format separate(cond , ...
written 3 months ago by Chirag Parsania • 1.4k
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Answer: C: how to create a fasta file with subset of sequences using seqinr
... Because you are not saving data in new object. Before you write in the file, you need to save in another object. See the change below. myfasta<- read.fasta(file = "MRP2.fas", seqtype = "AA",as.string = TRUE, set.attributes = FALSE) subsetlist<-read.table("list.txt", header=TRUE) ...
written 5 months ago by Chirag Parsania • 1.4k
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Answer: A: can i used RNA seq normalized data of PAAD, downloaded from TCGA with the help o
... 1. Is it normalized data ? You already mentioned in the question that ... > I downloaded the normalized RNA seq data of Pancreatic adenocarcinoma with the help of TCGA assember. Anyway, To me it seems normalised data. Typical FPKM/RPKM/TPM values looks like this (in the range of thousand). A ...
written 5 months ago by Chirag Parsania • 1.4k
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Answer: A: Add `chr` to first column of specific rows?
... ~ R way. dd <- tibble::tribble( ~V1, ~V2, ~V3, ~V4, ~V5, ~V6, ~V7, ~V8, ~V9, 1, "ensembl", "chromosome", 1, 300239041, ".", ".", ".", "ID=1;Name=chromosome:AGPv1:1:1:300239041:1", 1, "ensembl", ...
written 5 months ago by Chirag Parsania • 1.4k
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Answer: A: Plotting genes in terms of fold change in different grouping
... dd <- tibble::tribble( ~Gene, ~Fold_Change, ~Panel, ~TRG, "CHGA", -1.5652029, "Both", "TRG_4-5_Signature", "IL1B", -1.3159235, "Both", "TRG_4-5_Signature", "CXCL8", -1.231194003, "Both", "TRG_4-5_Signat ...
written 5 months ago by Chirag Parsania • 1.4k
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Answer: A: How to extract rows from data frame with row names in R?
... Solution given below. However, this is not bioinformatics question. dd <- readr::read_delim("example - Copy.csv" , delim = ",") out <- dd %>% dplyr::filter(INDIVIDUAL %in% c("IND" ,"IND1")) out # A tibble: 2 x 11 INDIVIDUAL pop M1 M2 M3 M4 M5 M6 M ...
written 5 months ago by Chirag Parsania • 1.4k

Latest awards to Chirag Parsania

Popular Question 4 days ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Popular Question 3 months ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Appreciated 3 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 3 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Scholar 5 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Appreciated 5 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 5 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Teacher 5 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 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
Appreciated 8 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 8 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Scholar 8 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
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
Guru 8 months ago, received more than 100 upvotes.
Supporter 8 months ago, voted at least 25 times.
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 to create 'gene' and 'transcript' entries in a GTF containing only exons
Autobiographer 8 months ago, has more than 80 characters in the information field of the user's profile.
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
Popular Question 10 months ago, created a question with more than 1,000 views. For Cross correlation analysis in R
Popular Question 10 months ago, created a question with more than 1,000 views. For Cross correlation analysis in R
Student 11 months ago, asked a question with at least 3 up-votes. For How to find intron co-ordinates from the gff file?
Student 12 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 ?
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