User: Thind

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Thind70
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Posts by Thind

<prev • 53 results • page 2 of 6 • next >
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Answer: A: Biomart Bioconductor - Retrieving All Entrezgenes Of Hsapiens_Gene_Ensembl
... Nowadays it is like "entrezgene_id" library(biomaRt) mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl") genes=getBM(attributes = c("hgnc_symbol", "entrezgene_id"), filters = "hgnc_symbol", values = all, bmHeader = TRUE, mart = mart) ...
written 10 weeks ago by Thind70 • updated 10 weeks ago by Kevin Blighe65k
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Comment: C: How to get fastq files for individual replicates?
... Better. contact to author and ask for clarification. sometimes researcher make mistakes at the time of submission. ...
written 11 weeks ago by Thind70
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Comment: C: Having trouble running ANNOVAR annotator for the first time please help!
... Check if the file "hg19_refGene.txt" exists or not. if yes, you can specify the path of the file manually. ...
written 11 weeks ago by Thind70
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Answer: A: How to process raw data (.cel files) from GEO and get annotation of genes
... [Geo2R][1] is the simplest option. After defining the groups in an online tool you can also download the R script for local use. For some platform, you may need to download the probes annotation file platform commercial website (Affymetrix or others). [https://www.biostars.org/p/96508/#443952][2] ...
written 11 weeks ago by Thind70
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Comment: C: How to get fastq files for individual replicates?
... usually, all the samples submitted within the specified project (three replicates means 6 fastq files (paired-end) ), [Here you can find the details of all the files of a project.][1] [1]: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SAMN06946596&o=acc_s%3Aa ...
written 11 weeks ago by Thind70
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Comment: C: Role of large/small sample size in adjusting p-value
... I understand the concept of p-value calculations but was confused that what they meant by "due to small sample size, p-values were not adjusted". I think you are right they didn't care about multiple-testing adjustment as you explained. Thanks. ...
written 12 weeks ago by Thind70
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Role of large/small sample size in adjusting p-value
... I read in one article that "due to small sample size, p-values were not adjusted". What is the role of the sample size in adjusting the p-value? I am trying to understand this in more details. Author was referring to MutSigCV tool output. ...
software error next-gen genomics snp statistics written 12 weeks ago by Thind70
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Comment: C: How many samples are good to find significant targets using GISTIC?
... Hi Kevin, I have a similar question. But in my study, I have a tumor sample size of 15. Do you think that I should use Gistic tool or is there any other way to represent the significance? and How I can apply something threshold for gain or loss explained at [Cosmic website.][1] You have any idea ...
written 12 weeks ago by Thind70
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Comment: C: How to download a GEO datafile
... Usually, options are available at the end of query page [check here][1] or You can use download it using various services here [Link][2] [1]: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE144239 [2]: https://www.ncbi.nlm.nih.gov/geo/info/download.html ...
written 3 months ago by Thind70
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Comment: C: GO enrichment analysis on my own gene list
... you can use [https://biit.cs.ut.ee/gprofiler/][1] or Cytoscape based CLuego AAP. [1]: https://biit.cs.ut.ee/gprofiler/ ...
written 3 months ago by Thind70

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Popular Question 4.4 years ago, created a question with more than 1,000 views. For Not able to retrieve PDB id from standalone blast against PDB

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