User: wangshx

gravatar for wangshx
wangshx10
Reputation:
10
Status:
New User
Location:
China/Shanghai/ShanghaiTech. University
Website:
http://bbs.sciencenet....
Last seen:
1 year, 10 months ago
Joined:
2 years, 8 months ago
Email:
w******@shanghaitech.edu.cn

I am a graduate student studying cancer research. I want to be  one  member of a great group to think how to code for better scientific research and deeply dig into ourselves.

Stay hungry, stay foolish.

 

Posts by wangshx

<prev • 15 results • page 1 of 2 • next >
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Difference between MultiSet and ExpressionSet class
... ExpressionSet is very common and useful,here I have a question about the difference between the MultiSet class and ExpressionSet class. The [reference](http://www.bioconductor.org/packages/release/bioc/manuals/Biobase/man/Biobase.pdf) tells that > Container for high-throughput assays and exper ...
R bioconductor biobase written 23 months ago by wangshx10
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Comment: C: How can I reassign assayData slot of ExpressionSet?
... Thank a lot. Your suggestion is practical. ...
written 23 months ago by wangshx10
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How can I reassign assayData slot of ExpressionSet?
... When I use `exprs` function to reassign expression matrix to an `ExpressionSet` object, it does not work and an error occur. I want to remove the rows which cannot match any `gene symbol`. A minimal code as follows can reproduce my error, someone who know how to do this correctly please help me, t ...
bioconductor microarray biobase written 23 months ago by wangshx10 • updated 23 months ago by Kevin Blighe52k
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Comment: C: Hg19 regions for Intergenic, Promoters, Enhancer, Exon, Intron, 5-UTR, 3-UTR and
... cut -f 6 genome_feature.bed | sort | uniq CDS EXON INTRON TRANSCRIPT UTR Only have 5 features, I am curious about how can I get gene and intergenic regions? How to differ 5' UTR and 3' UTR? The tools is really awesome. Thanks. ...
written 2.2 years ago by wangshx10
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Comment: C: What does the X_OS_IND column of Phenotypes mean?
... sorry, I just want to figure out this question. ...
written 2.4 years ago by wangshx10
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What does the X_OS_IND column of Phenotypes mean?
... Question I have posted on https://bioinformatics.stackexchange.com/questions/2097/what-does-the-x-os-ind-column-mean. ...
R file format written 2.4 years ago by wangshx10 • updated 2.4 years ago by Biostar ♦♦ 20
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Comment: C: `chromosome_strand` all change to `1`
... $zcat simple_somatic_mutation.open.tsv.gz |head -5 icgc_mutation_id icgc_donor_id project_code icgc_specimen_id icgc_sample_id matched_icgc_sample_id submitted_sample_id submitted_matched_sample_id chromosome chromosome_start chromosome_end chromosome_strand assembly_version mutation_type r ...
written 2.4 years ago by wangshx10
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`chromosome_strand` all change to `1`
... The `chromosome_strand` column should indicate "-" or "+". It is right when I use `zcat simple_somatic_mutation.open.tsv.gz |head -5` to see the head of data (from ICGC tsv file). But when I use `awk` to get some columns I am interested in, `chromosome_strand` all change to `1`. Anybody know why? ...
icgc awk written 2.4 years ago by wangshx10
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Comment: C: why gtf file has 0 length of CDS region
... It is new for me that exists 1 base long microexons. ...
written 2.4 years ago by wangshx10
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why gtf file has 0 length of CDS region
... I retrieve CDS region from `gtf` file (ensembl v75). When I check the region length of CDS, I am very curious about the following result library(data.table) annotation <- fread('Homo_sapiens.GRCh37.75.gtf') > summary(annotation[annotation$V3=="CDS",]$V5 - annotation[ann ...
genome R annotation written 2.4 years ago by wangshx10 • updated 2.4 years ago by Devon Ryan93k

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