User: user_g

gravatar for user_g
user_g20
Reputation:
20
Status:
New User
Location:
Last seen:
5 months, 3 weeks ago
Joined:
2 years, 5 months ago
Email:
g***********@lau.edu

Posts by user_g

<prev • 17 results • page 1 of 2 • next >
0
votes
0
answers
191
views
0
answers
Annotating entrez Ids with the kegg pathway they are involved in
... Hello, I have a list of entrez Ids I would like to map them to their relative kegg pathways. So for every genes I would like to have a kegg pathway reference to which it is involved in. Is there a package that can help me do this in R? Thank you! ...
kegg pathway R semantic similarity entrez kegg written 6 months ago by user_g20
2
votes
0
answers
298
views
0
answers
(Closed) Creating Nice R vignettes
... Hello, I am writing my first bioconductor package so I do not have much information on the format required. I am following the vignette format which is built with R studio. However I am seeing some vignettes which have a some text color and a different format, does anyone know how to achieve this? ...
vignettes R written 16 months ago by user_g20
1
vote
0
answers
383
views
0
answers
Error in RCircos.Validate.Genomic.Data:One or more genomic position in plot data is outside of chromosome length for Mchr5.
... Hello, I have the following data which I want to plot on Rcircus and link them. srcTName srcTStart srcTEnd SeqNames Start End 1 Hchr18 657287 658525 Mchr5 30072897 30073562 2 Hchr18 830267 830721 Mchr5 32594399 32594708 3 Hchr18 903627 905104 Mchr1 ...
rcircus R written 17 months ago by user_g20 • updated 17 months ago by RamRS25k
0
votes
0
answers
1.2k
views
0
answers
Comment: C: R/Circos, cannot make inter-chromosomal links to multiple chromosomes.
... Hello, I am having the same problem now. Did you manage to make it work? ...
written 17 months ago by user_g20
0
votes
0
answers
309
views
0
answers
(Closed) Creating files within R code
... Hello, I am writing an R code which uses kentUtils . The tools from kentUtils create temporary files which are required for the code to progress, this code will be given to other users to use. My question is what is the most appropriate way to deal with these files through the R code. Should I ...
R rstudio kentutils written 17 months ago by user_g20
0
votes
0
answers
233
views
0
answers
kentUtils bedToPsl -keepQuery
... Hello, I am using kentUtils bedToPsl inorder to convert a bed file to psl file inorder to map the results using pslMap. There is an option in bedToPsl ***-keepQuery*** Their documentation says : ***-keepQuery - instead of creating a fake query, create PSL with identical query and target spe ...
bedtopsl kentutils written 17 months ago by user_g20
0
votes
1
answer
425
views
1
answers
Comment: C: Clustering coordinates based on window size
... Thank you! I will try it ...
written 19 months ago by user_g20
0
votes
0
answers
536
views
0
answers
Comment: C: Splitting a dataframe into overlapping groups of equal sizes
... hello, yes I tried using the for loop but when dealing with large data, it became very slow this is why I am looking for another way ...
written 19 months ago by user_g20
1
vote
1
answer
425
views
1
answer
Clustering coordinates based on window size
... Hello, I am writing a script that can detect clusters of transcription factors found within a certain window size. The code can read bed files and the user has the option to choose how many transcription factor binding sites he wants within this window. The aim is also to allow (or prevent) certai ...
iranges R genomicranges granges written 19 months ago by user_g20 • updated 19 months ago by Alex Reynolds29k
0
votes
0
answers
536
views
0
answers
Comment: C: Splitting a dataframe into overlapping groups of equal sizes
... I am alternating between data frames and GRanges to find the perfect way to achieve this, so I if I could find a way to do this in GRanges then I will convert my data frame into a GRange object. Yes the same row can be in another group. Yes thats true, I will end up having the same number of clust ...
written 19 months ago by user_g20

Latest awards to user_g

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1898 users visited in the last hour