User: Shian Su

gravatar for Shian Su
Shian Su20
Reputation:
20
Status:
New User
Location:
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Last seen:
1 week, 1 day ago
Joined:
3 years, 9 months ago
Email:
s***@wehi.edu.au

Posts by Shian Su

<prev • 16 results • page 1 of 2 • next >
0
votes
1
answer
98
views
1
answer
Should GenomicAlignments::mapToAlignments() terminate when no alignments are found for one read?
... When using mapToAlignments() with multiple GAlignments, it appears to terminate if none of the query GRanges map to a GAlignment. library(GenomicAlignments) alignments <- GAlignments( c("chr1", "chr1"), c(20L, 10L), c("11M", "11M"), strand(c("*", "*")), ...
genomicalignments written 5 weeks ago by Shian Su20 • updated 4 weeks ago by Valerie Obenchain6.7k
0
votes
1
answer
136
views
1
answers
Comment: C: How to query a base along an aligned read by genomic position?
... > The names are required since the mapped return value needs to use the > read identifiers as its seqnames. What is the meaning of seqnames here? I thought seqname generally referred to the molecule name (chromosome/transcript). ...
written 5 weeks ago by Shian Su20
0
votes
1
answer
136
views
1
answers
Comment: C: How to query a base along an aligned read by genomic position?
... Thanks Herve, this is very close to what I want to do. It does a great job mapping from the reference coordinates to the query coordinate. The only issue now is that GAlignments, as far as I can tell, doesn't have the ability to read in the sequence and quality scores, so to query the actual base I ...
written 6 weeks ago by Shian Su20
4
votes
1
answer
136
views
1
answer
How to query a base along an aligned read by genomic position?
... I am trying to haplotype long reads after aligning to the genome. To do this I would need to find out what bases are at annotated variant sites, which should be possible using a combination of the alignment position, the sequence and the CIGAR string. I am wondering if there are already facilities i ...
genomicalignments bam cigar written 6 weeks ago by Shian Su20 • updated 5 weeks ago by Janet Young740
0
votes
1
answer
137
views
1
answers
Comment: C: What to do when a bug is found in a BioConductor package (Glimma)
... Thanks for the bug report Samuel. As Gordon mentioned, I would prefer bugs be submitted through Github issues. The reason for the bug is that I've rounded all values to 4 significant places to avoid values with tens of digits, it's clear that this causes confusion for large numeric values so I'll up ...
written 3 months ago by Shian Su20
0
votes
1
answer
292
views
1
answers
Answer: A: Why does the Glimma package require R >= 3.4.0 ?
... It doesn’t use any features from the latest R release, however it is Bioconductor policy to use require the latest R version on all packages. If you know how to change the dependency in the DESCRIPTION file then the package will work perfectly fine on an older version of R. ...
written 21 months ago by Shian Su20
0
votes
1
answer
1.4k
views
1
answers
Comment: C: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
... Thanks Johannes, that's very helpful. Do you know if there are any major differences between the AH##### databases and Homo.sapiens that I should be aware of? ...
written 2.1 years ago by Shian Su20
5
votes
1
answer
1.4k
views
5 follow
1
answer
Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapiens/Mus.musculus?
...   I'm trying to use Homo.sapiens to annotate genes from my count matrix. However I never seem to find any genes from chrM. library(Homo.sapiens) all_genes <- biomaRt::select( Homo.sapiens, key = keys(Homo.sapiens, keytype = "GENEID"), keytype = "GENEID", columns = c("CDSCHROM" ...
annotationdbi homo.sapiens written 2.1 years ago by Shian Su20 • updated 2.1 years ago by Johannes Rainer1.5k
0
votes
1
answer
941
views
1
answers
Comment: C: Cannot create SingleCellExperiment object
... Thanks Aaron, following that other question thread lead me to the solution. I had been drawing most of the BioC packages from a shared location I have no access to. The solution was to use biocLite("SingleCellExperiment", dependencies=TRUE, lib="~/R/library") to get a copy of all the dependencies ...
written 2.1 years ago by Shian Su20
3
votes
1
answer
941
views
1
answer
Cannot create SingleCellExperiment object
...   Using R 3.4.2, BioC 3.6, SingleCellExperiment_1.0.0. The following example code from ?SingleCellExperiment produces an error   library(SingleCellExperiment) ncells <- 100 u <- matrix(rpois(20000, 5), ncol=ncells) v <- log2(u + 1) pca <- matrix(runif(ncells*5), ncells) tsne <- ...
singlecellexperiment written 2.1 years ago by Shian Su20 • updated 2.1 years ago by Aaron Lun25k

Latest awards to Shian Su


Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 178 users visited in the last hour