User: darklings

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darklings150
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Posts by darklings

<prev • 31 results • page 1 of 4 • next >
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Answer: A: Incomplete reactome.org all pathway level to ENSEMBL ID annotation files
... There is an R package (https://github.com/reactome/ReactomeContentService4R) which is the wrapper for the Reactome Content Service API. Mapping an ESID (`ENSG00000282120` in the question) to Reactome Pathway(s): library(ReactomeContentService4R) #> Connecting...welcome to Reactome v74! ...
written 4 weeks ago by darklings150
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Comment: C: Is it good to merge transcripts tpm to gene which is of different gene type?
... Yea, usually we use tximport or [tximeta](https://bioconductor.org/packages/devel/bioc/vignettes/tximeta/inst/doc/tximeta.html) to get the gene-level values ...
written 4 weeks ago by darklings150
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Answer: A: How can I know when a pathway was included in Reactome?
... 2020: Try the [`ReactomeContentService4R`](https://github.com/reactome/ReactomeContentService4R) R package interfacing with the newest Reactome database: To get gene symbols of the pathway `R-HSA-2559583`: devtools::install_github("reactome/ReactomeContentService4R") library(ReactomeConten ...
written 5 weeks ago by darklings150
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Comment: C: Is there a way to get the name or IDs of genes with the goseq table?
... I am not sure, maybe `getgo()` doesn't support your genome. Could you provide a bit more details about your species and code/error? ...
written 9 months ago by darklings150
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Comment: C: Getting information about shortening or lengthening of UTRs from RNAseq data
... Some other tools first identify de novo APA sites from RNA-seq and then test which genes have shortening or lengthening UTRs. I tried QAPA and another labmate tried DaPars, and the results are quite different... ...
written 11 months ago by darklings150
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Comment: C: output TMM normalized counts with edgeR
... Hi, I am wondering why the `estimateTagwiseDisp()` is needed? Does it change anything for the output? ...
written 11 months ago by darklings150
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Comment: C: How to interpret the eQTLs in cancer
... Oh wow thanks, now I am a bit confused about why I asked this question at that time... ...
written 12 months ago by darklings150
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Comment: C: Best-suited unit of expression to perform between-sample comparison
... should be the `cpm()` function? ...
written 16 months ago by darklings150
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Comment: C: Best-suited unit of expression to perform between-sample comparison
... What if I need something accounts for gene length and intersample differences? Could I do between sample normalization, like TMM, on TPM values? ...
written 16 months ago by darklings150
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Answer: A: genefu for PAM50 prediction
... Values that have been normalized and transformed for between sample comparison are appropriate. I use the expression data that are median ratio normalized and variance stabilizing transformed (functions in DESeq2) from the read counts to do the PAM50 classification, then I compared the results pred ...
written 17 months ago by darklings150

Latest awards to darklings

Teacher 5 weeks 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?
Popular Question 7 months ago, created a question with more than 1,000 views. For How to analyze the variants in non-coding regions
Popular Question 8 months ago, created a question with more than 1,000 views. For What cause the differences between genes annotations from different databases?
Popular Question 8 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 8 months ago, voted at least 25 times.
Teacher 14 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 16 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 23 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 2.6 years ago, created a question with more than 1,000 views. For Intersect vcf file and bed file

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