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User: Chirag Parsania

gravatar for Chirag Parsania
Chirag Parsania • 1.3k
Reputation:
1,320
Status:
Trusted
Location:
University of Macau
Scholar ID:
Google Scholar Page
Last seen:
4 days, 23 hours ago
Joined:
3 years, 7 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 • 169 results • page 1 of 17 • next >
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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 weeks ago by Chirag Parsania • 1.3k
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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 weeks ago by Chirag Parsania • 1.3k
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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 weeks ago by Chirag Parsania • 1.3k
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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 weeks ago by Chirag Parsania • 1.3k
2
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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 6 weeks ago by Chirag Parsania • 1.3k
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Comment: C: How to plot a profile showing read coverage around the 5 prime splice site?
... You can use function `flank`. See the example below. I am using data from the same example given in previous reply. tes_flank <- flank(genes, start = FALSE ,width = 5, both = TRUE) ## setting start = FALSE gives flank co-ordinated form the end (3' region if you give genes for input). Setti ...
written 6 weeks ago by Chirag Parsania • 1.3k
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Comment: C: How to plot a profile showing read coverage around the 5 prime splice site?
... Hi, I use R package `GenomicFeatures` to deal with gff. See example below to get co-ordinates from gff using `GenomicFeatures`. I used `Candida glabrata` gff file for example purpose. gff_file <- "C_glabrata_CBS138_version_s02-m07-r06_features.gff" gff <- GenomicFeatures::makeTxDbFro ...
written 6 weeks ago by Chirag Parsania • 1.3k
0
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368
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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 11 weeks ago by Chirag Parsania • 1.3k
1
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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 3 months ago by Chirag Parsania • 1.3k
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Comment: C: How to plot a profile showing read coverage around the 5 prime splice site?
... I would suggest to take all the isoforms for a given gene. The reason for that is anyway you want to look at overall profile between the conditions. So, If there are any differences, it will be shown up in profile. However, if you want to do the same analysis at gene level, then you can think of con ...
written 3 months ago by Chirag Parsania • 1.3k

Latest awards to Chirag Parsania

Scholar 4 weeks ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Appreciated 5 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 5 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 3 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Teacher 3 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 4 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 4 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
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
Guru 4 months ago, received more than 100 upvotes.
Supporter 4 months ago, voted at least 25 times.
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
Autobiographer 4 months ago, has more than 80 characters in the information field of the user's profile.
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
Popular Question 6 months ago, created a question with more than 1,000 views. For Cross correlation analysis in R
Popular Question 6 months ago, created a question with more than 1,000 views. For Cross correlation analysis in R
Student 7 months ago, asked a question with at least 3 up-votes. For How to find intron co-ordinates from the gff file?
Student 8 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 8 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Reorder heatmap rows in a dataset with missing values
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Reorder heatmap rows in a dataset with missing values
Good Answer 9 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 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
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