User: darklings

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darklings90
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Posts by darklings

<prev • 28 results • page 2 of 3 • next >
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Comment: C: issues with GTEx data annotation files
... The file is tab delimited, go check your excel `Data` -> `Text to Columns` ...
written 18 months ago by darklings90
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Answer: A: Is there a way to get the name or IDs of genes with the goseq table?
... Yes please refer to this post: https://support.bioconductor.org/p/102273/ For my own case, I modified the function # Get the gene lists of "numDFinCat" in GO.wall report getGeneLists <- function(pwf, goterms, genome, ids){ gene2cat <- getgo(rownames(pwf), genome, ids) cat ...
written 18 months ago by darklings90
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How to interpret the eQTLs in cancer
... According to the paper [PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types][1], they conducted the eQTL mapping using RNA-seq and genotype data from TCGA. I am a bit confused about the meaning of cancer eQTL. I know that an eQTL is a locus that explains a fraction ...
tcga rna-seq snp eqtl written 18 months ago by darklings90 • updated 7 months ago by cao5109270
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Comment: C: How To Update R In Ubuntu ?
... Update R version (3.4 -> 3.5) in Ubuntu 16.04 (xenial): sudo su echo "deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran35/" >> /etc/apt/sources.list apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 apt-get update apt-get install r-base ...
written 20 months ago by darklings90
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Comment: C: What kind of read counts of RNA-seq should be used in machine learning models?
... Thanks for the reminder, but what should be removed priorly for highly correlated data? ...
written 20 months ago by darklings90
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Comment: C: rsID and its link with disease/traits/phenotype
... You can just simply type your question title on google then find some links like this: https://preview.ncbi.nlm.nih.gov/guide/howto/find-human-variations-with-phenotype/ or just to google the rsIDs that you are interested in, also Ensembl biomart is worth exploring. For a bunch of IDs, using tools ...
written 20 months ago by darklings90
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Answer: A: What kind of read counts of RNA-seq should be used in machine learning models?
... I found the posts: [FPKM or rlog from DEseq2 for machine learning analysis][1] [Log expression for machine learning input][2] The cross-sample normalized log counts were recommended for downstream machine learning techniques, however I need to add the counts of sets of genes as features, maybe I ...
written 20 months ago by darklings90
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What kind of unit of RNA-seq should be used in machine learning models?
... I want to train a binary classifier using cancer RNA-seq data. After differential expression analysis, I selected some top DEGs as features for glmnet training, however the performances were quite bad, I think this may be due to tumor heterogeneity. Therefore I plan to do feature engineering, like ...
machine learning rna-seq counts written 20 months ago by darklings90
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Comment: C: How to retrieve Ensembl phenotype data associated with Ensembl variations using
... Thank you so much Ben, I will know better next time ...
written 2.7 years ago by darklings90
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How to retrieve Ensembl phenotype data associated with Ensembl variations using Perl API
... I have retrieved all variants in a single chromosome using the slice adapter and variation feature adaptor, then I got a file that contains variant ids and other basic information, looks like: rs867361848 A/G 10010 10010 SNV dbSNP rs370048753 A/T 10014 10014 SNV ...
ensembl perl api written 2.7 years ago by darklings90 • updated 2.7 years ago by Ben_Ensembl1.5k

Latest awards to darklings

Popular Question 11 weeks ago, created a question with more than 1,000 views. For How to analyze the variants in non-coding regions
Popular Question 3 months ago, created a question with more than 1,000 views. For What cause the differences between genes annotations from different databases?
Popular Question 3 months ago, created a question with more than 1,000 views. For What kind of unit of RNA-seq should be used in machine learning models?
Supporter 3 months ago, voted at least 25 times.
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Is there a way to get the name or IDs of genes with the goseq table?
Scholar 12 months ago, created an answer that has been accepted. For A: Is there a way to get the name or IDs of genes with the goseq table?
Scholar 18 months ago, created an answer that has been accepted. For A: Is there a way to get the name or IDs of genes with the goseq table?
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Intersect vcf file and bed file

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