User: Chirag Parsania

gravatar for Chirag Parsania
Chirag Parsania1.4k
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Location:
University of Macau
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Last seen:
14 hours ago
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4 years 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 • 178 results • page 2 of 18 • next >
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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 6 months ago by Chirag Parsania1.4k
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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 6 months ago by Chirag Parsania1.4k
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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 6 months ago by Chirag Parsania1.4k
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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 6 months ago by Chirag Parsania1.4k
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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 months ago by Chirag Parsania1.4k
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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 months ago by Chirag Parsania1.4k
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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 7 months ago by Chirag Parsania1.4k
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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 8 months ago by Chirag Parsania1.4k
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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 8 months ago by Chirag Parsania1.4k
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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 8 months ago by Chirag Parsania1.4k

Latest awards to Chirag Parsania

Epic Question 20 days ago, created a question with more than 10,000 views. For Z-Score calculation by heatmap.2
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Popular Question 4 months ago, created a question with more than 1,000 views. For Extract reads from bam/sam files using read id
Scholar 5 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Scholar 6 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
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
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
Scholar 9 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Scholar 9 months ago, created an answer that has been accepted. For A: GO enrichment - interpreting broad terms
Teacher 9 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 9 months ago, received more than 100 upvotes.
Supporter 9 months ago, voted at least 25 times.
Teacher 9 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 9 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 9 months ago, has more than 80 characters in the information field of the user's profile.
Teacher 10 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 11 months ago, created a question with more than 1,000 views. For Cross correlation analysis in R
Popular Question 12 months ago, created a question with more than 1,000 views. For Cross correlation analysis in R
Student 12 months ago, asked a question with at least 3 up-votes. For How to find intron co-ordinates from the gff file?

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