User: Prakash

gravatar for Prakash
Prakash1.7k
Reputation:
1,680
Status:
Trusted
Location:
India
Twitter:
gprakash047
Last seen:
1 day, 6 hours ago
Joined:
4 years, 3 months ago
Email:
j********@gmail.com

Posts by Prakash

<prev • 131 results • page 1 of 14 • next >
1
vote
1
answer
145
views
1
answers
Comment: C: export picture from R studio
... you could try to take output in a file and see if its generating some plot plot.pdf("plot") see.genes(get$sig.genes, k = 8) dev.off() ...
written 8 weeks ago by Prakash1.7k
1
vote
0
answers
162
views
0
answers
Comment: C: Extracting START and STOP codon position from Augustus GFF
... you can simply use `grep` command to extract the line. grep "start_codon" file ...
written 8 weeks ago by Prakash1.7k
0
votes
0
answers
201
views
0
answers
Comment: C: feature count at gene and transcript level
... What I understood that there is some issue with NCBI REFseq GTF file downloaded from UCSC table browser. The second GTF file having gene symbol as gene_id i generated using following line of code rsync -a -P rsync://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/refGene.txt.gz ./ gzip -d ...
written 8 weeks ago by Prakash1.7k
3
votes
1
answer
117
views
1
answers
Answer: C: Chip seq coverage
... [deepTools][1] [1]: https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html ...
written 8 weeks ago by Prakash1.7k
0
votes
0
answers
201
views
0
answers
Comment: C: feature count at gene and transcript level
... Actually both the gtf file were downloaded from [UCSC table browser][1], First one is NCBI refseq track from table UCSC Refseq (refgene) downloaded as GTF file and second one downloaded as "all fields from selected table" and further converted to GTF format using `genePredToGtf` I checked several ...
written 8 weeks ago by Prakash1.7k
2
votes
0
answers
201
views
0
answers
feature count at gene and transcript level
... Hi all, I have aligned my RNAseq data to the reference genome and extracted raw count using `featureCounts` tool. I used two different GTF file from NCBI, one having only Refseq id as gene_id and other having gene symbol as gene_id. Refseq as gene_id > chr11 mm10_refGene exon 1008838 ...
rna-seq written 8 weeks ago by Prakash1.7k
0
votes
1
answer
193
views
1
answers
Comment: C: scale in R pheatmap
... yes, of course. you may try it row for clustering row-wise. ...
written 10 weeks ago by Prakash1.7k
3
votes
1
answer
193
views
1
answers
Answer: C: scale in R pheatmap
... scale function is used to transform the values. values are scaled using mean and standard deviation ([link][1]). While clustering, scaling is generally performed to obtain better cluster. clustering would change based on other parameters also such as distance method. [1]: https://www.r-bloggers ...
written 10 weeks ago by Prakash1.7k
3
votes
2
answers
187
views
2
answers
Answer: A: Need help with simple FOR loop
... I would try two things here. create a list and push the values immune =list() for (i in 0:14){ immune[i] =FindMarkers(AllCells.combined, ident.1 = "VEH", ident.2 = "IMQ", verbose = TRUE, group.by="stim", subset.ident = i) ) } #or create multiple object using loop for ...
written 12 weeks ago by Prakash1.7k
0
votes
1
answer
253
views
1
answers
Comment: C: Motif analysis from H3K27ac ChIPseq broad peaks
... Thanks @Venu for your insight. This was helpful. The reason using `broad` option is that histone acetylation marks covers broad regions (~1kb). I tried calling both using `narrow` and `broad` options, in my case also the narrow peaks seems working well. As per your suggestion i can use narrow peaks ...
written 12 weeks ago by Prakash1.7k

Latest awards to Prakash

Teacher 29 days ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Delete numbers in the tables column
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: How to add colors to bar chart?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Error while running computeMatrix of deepTools
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Appreciated 3 months ago, created a post with more than 5 votes. For A: How to add colors to bar chart?
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: How to add gene symbol to RNA-Seq data using R
Appreciated 3 months ago, created a post with more than 5 votes. For A: Delete numbers in the tables column
Appreciated 4 months ago, created a post with more than 5 votes. For A: How to add colors to bar chart?
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: How to add gene symbol to RNA-Seq data using R
Scholar 4 months ago, created an answer that has been accepted. For A: How to add colors to bar chart?
Appreciated 4 months ago, created a post with more than 5 votes. For A: How to add colors to bar chart?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Scholar 4 months ago, created an answer that has been accepted. For A: How to add colors to bar chart?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Delete numbers in the tables column
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How to add gene symbol to RNA-Seq data using R
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Appreciated 6 months ago, created a post with more than 5 votes. For A: How to add colors to bar chart?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How to add colors to bar chart?
Guru 7 months ago, received more than 100 upvotes.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1548 users visited in the last hour