User: piyushjo

gravatar for piyushjo
piyushjo160
Reputation:
160
Status:
Trusted
Location:
Last seen:
an hour ago
Joined:
1 year, 3 months ago
Email:
p*******@gmail.com

Posts by piyushjo

<prev • 73 results • page 1 of 8 • next >
0
votes
2
answers
113
views
2
answers
Comment: C: GenBank accesion number to gene id
... Could list at least 5 examples of genbank and other gene id you are referring to? ...
written 1 day ago by piyushjo160
0
votes
2
answers
80
views
2
answers
Answer: A: Extracting important gene with similar expression level from multiple samples
... You can try WGCNA. It will help you select non-linearly correlated genes. I am just concerned with such a small sample cohort you have. https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/ For your second analysis you can use mutual information based analysis. For that you ...
written 1 day ago by piyushjo160
0
votes
2
answers
113
views
2
answers
Comment: C: GenBank accesion number to gene id
... Yes, sorry. It looks like while ensembl has a page your organism it doesn't show up in the biomart. http://bacteria.ensembl.org/Pseudomonas_aeruginosa_pa14/Info/Index ...
written 1 day ago by piyushjo160
0
votes
2
answers
113
views
2
answers
Answer: A: GenBank accesion number to gene id
... Biomart from ensembl.org has such features. You can convert any given id to another id. I see the you organism has an ensembl page. I think you could use the biomaRt package in R and follow the example for human data from below vignette. https://bioconductor.org/packages/release/bioc/vignettes/bio ...
written 1 day ago by piyushjo160
0
votes
2
answers
125
views
2
answers
Answer: A: To generate an scRNA counts file using barcodes.tsv, genes.tsv and matrix.mtx fi
... You can follow the instruction on the following webpage with the heading "Loading matrices into R". https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices It will generate what is called a "sparse-matrix". Then you convert the sparse-matrix (SM) into ...
written 1 day ago by piyushjo160
2
votes
1
answer
57
views
1
answers
Answer: A: Upstream regulators of a gene/protein
... One way to do it is to use STRINGdb. They have various type of interaction information. The annotation will also tell you what the presumed interaction is and the level of evidence. The second is to use Ingeniuty Pathway Analysis. However, this is a paid service. You can get similar information, bu ...
written 2 days ago by piyushjo160
2
votes
2
answers
91
views
2
answers
Answer: A: Get a bunch of ENTREZID into gene symbols
... Try biomart. Website https://useast.ensembl.org/info/data/biomart/index.html R package https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/biomaRt.html Use Gene symbol as filter and then entrez id as attribute. ...
written 7 days ago by piyushjo160
0
votes
2
answers
95
views
2
answers
Comment: C: Find similar values in two gene lists
... You first need to have files with those name in the folder. list1 and list2 are the two lists that have given in your example. ...
written 9 days ago by piyushjo160
0
votes
2
answers
95
views
2
answers
Comment: C: Find similar values in two gene lists
... You have to add description as a comment and not as answer. ...
written 10 days ago by piyushjo160
0
votes
2
answers
95
views
2
answers
Answer: A: Find similar values in two gene lists
... Try this list1<-read.delim("1_10.txt") list2<-read.delim("1_10.txt") Here both of your lists are exactly same. Do you have long list of genes in two files or is it a matrix? The following will work for a list with one column. First convert factors into characters array list1&l ...
written 10 days ago by piyushjo160

Latest awards to piyushjo

Scholar 3 days ago, created an answer that has been accepted. For A: Get a bunch of ENTREZID into gene symbols
Popular Question 3 months ago, created a question with more than 1,000 views. For How different is rlog transformation from vst transformation in DESeq2

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1613 users visited in the last hour