User: MatthewP

gravatar for MatthewP
MatthewP410
Reputation:
410
Status:
Trusted
Location:
China
Last seen:
3 hours ago
Joined:
1 year, 10 months ago
Email:
m***********@gmail.com

Posts by MatthewP

<prev • 142 results • page 1 of 15 • next >
2
votes
4
answers
123
views
4
answers
Answer: A: Conversion of Gene Name to Ensemble ID
... Hello, here is some way I know. 1. R package [org.Hs.eg.db](http://bioconductor.org/packages/3.9/data/annotation/html/org.Hs.eg.db.html), this package contains mapping between gene IDs, like SYMBOL, entrez ID, Ensembl ID. 2. R package [biomaRt](https://bioconductor.org/packages/release/bioc/html ...
written 3 days ago by MatthewP410
0
votes
0
answers
121
views
0
answers
Comment: C: DEGS analysis with DESeq2?
... Can you show us your `StringTie` command? ...
written 5 days ago by MatthewP410
0
votes
0
answers
69
views
0
answers
Comment: C: How to get negative 2 ks test D value in R?
... Yes I know how to get `D` value. My problem is there is no negative `D` value as the paper said "A sample with a positive EMT score exhibits a more Mes phenotype, whereas a negative EMT score reflects a more Epi phenotype.". `ks.test` function return positive `D` value or 0. ...
written 22 days ago by MatthewP410
0
votes
0
answers
69
views
0
answers
How to get negative 2 ks test D value in R?
... Hello, here is an EMT score method > The empirical cumulative distribution function (ECDF) was estimated for Epi and Mes gene sets. The 2KS test was employed to compute the difference between Mes ECDF (ECDFMes) and Epi ECDF (ECDFEpi). The 2KS score was then taken as the EMT score. A sample with a ...
statics rna-seq written 22 days ago by MatthewP410
0
votes
1
answer
839
views
1
answers
Comment: C: TCGA TMB: What exome size to use?
... Hello, `mutation-load-updated.txt` is log10 scale data? If I want TMP data do I need too sum silent and non-silent together? ...
written 5 weeks ago by MatthewP410
0
votes
1
answer
1.3k
views
1
answers
Comment: C: WGCNA exportNetworkToCytoscape issue!!
... Hello, I know WGCNA use TOM , the function `exportNetworkToCytoscape` needs adjacency matrix as input. It's TOM suits here? ...
written 6 weeks ago by MatthewP410
0
votes
0
answers
96
views
0
answers
Comment: C: How maftools oncoplot classify variant type?
... Ok, set `writeMatrix = TRUE` when using `maftools::oncoplot` function will get oncoplot data, no need to extract byhand. But I will leave question in case some have same problem. ...
written 8 weeks ago by MatthewP410
0
votes
0
answers
96
views
0
answers
How maftools oncoplot classify variant type?
... Hello, I need to draw oncoplot with `ComplexHeatmap` instead of use `oncoplot` function in `maftools` for some reason. So I first need to extract plot data from `maftools`. pradMaf <- read.maf("/Work/Mutect2.maf") # get top 20 genes geneSummary <- getGeneSummary(pradMaf)[1:20,] ...
maftools written 8 weeks ago by MatthewP410
0
votes
0
answers
168
views
0
answers
Seeks good way to convert GB_LIST to SYMBOL
... Take `GPL5188` as example. This GPL map probe id to GB_LIST(genebank). > gpl <- getGEO("GPL5188", AnnotGPL=FALSE, destdir=".") > as_tibble(Table(gpl)) %>% dplyr::select(ID, GB_LIST) %>% head(n = 3) # A tibble: 3 x 2 ID GB_LIST ...
geo written 11 weeks ago by MatthewP410
1
vote
3
answers
239
views
3
answers
Answer: A: Building Dict File for GATK
... Run GATK command `gatk command` if gatk is installed, you can run `gatk CreateSequenceDictionary` in your case. Or java -jar gatk.jar command like `java -jar gatk-package-4.1.4.1-local.jar CreateSequenceDictionary`. You don't have to always follow the gatk example command, picard is inside gatk. ...
written 11 weeks ago by MatthewP410

Latest awards to MatthewP

Popular Question 11 days ago, created a question with more than 1,000 views. For How to use snpSift annotate -info option to annotate specific fields of INFO
Popular Question 26 days ago, created a question with more than 1,000 views. For How to use snpSift annotate -info option to annotate specific fields of INFO
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Some questions about write human mitochondrial variants into VCF file
Scholar 3 months ago, created an answer that has been accepted. For A: How to convert data from NCBI E-utilities.efetch to python data object?
Scholar 3 months ago, created an answer that has been accepted. For A: How to convert data from NCBI E-utilities.efetch to python data object?
Scholar 4 months ago, created an answer that has been accepted. For A: How to convert data from NCBI E-utilities.efetch to python data object?
Centurion 5 months ago, created 100 posts.
Scholar 7 months ago, created an answer that has been accepted. For A: How to convert data from NCBI E-utilities.efetch to python data object?
Appreciated 8 months ago, created a post with more than 5 votes. For A: Problem with downloading GSE file by GEOquery
Scholar 8 months ago, created an answer that has been accepted. For A: How to convert data from NCBI E-utilities.efetch to python data object?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Problem with downloading GSE file by GEOquery
Scholar 14 months ago, created an answer that has been accepted. For A: How to convert data from NCBI E-utilities.efetch to python data object?
Supporter 14 months ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1056 users visited in the last hour