User: mk

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mk110
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Posts by mk

<prev • 33 results • page 1 of 4 • next >
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Comment: C: censoring time for ICGC records with no followup or date of death?
... Indeed, I will update once I receive a response from their support team. ...
written 2 days ago by mk110
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Comment: C: ICGC mRNA sequencing data: where is the documentation on analysis_id?
... Thanks, Kevin I have emailed support. They are swamped due to lock down. Agree regarding the abbreviation, that's how I am proceeding in the mean time. ...
written 6 days ago by mk110
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censoring time for ICGC records with no followup or date of death?
... Looking at the ICGC release of PACA-CA (various stages of pancreatic carcinoma, Canada) there are numerous censored records (no death date) without a followup time. Is there a default censoring time for ICGC studies? Here are some examples ([PACA-CA][1]): patient ID | followup | death time ...
icgc survival cancer written 7 days ago by mk110
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Comment: C: Entrez e-utils reference for ensembl ids
... awesome, didn't know that ENSG ids were accepted ...
written 13 days ago by mk110
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ICGC mRNA sequencing data: where is the documentation on analysis_id?
... If you check the release file "gene_expression" for e.g. [PACA-CA (pancreatic carcinoma, Canada)][1], there is a column "analysis_id". In this case the value is [PACA-CA_RNA0, PACA-CA_WTS]. Is there documentation anywhere that explains what this indicator means? [1]: https://dcc.icgc.org/relea ...
icgc rna-seq written 14 days ago by mk110
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Entrez e-utils reference for ensembl ids
... I know this is a long shot, but assuming my access to services is limited to e-utils, is there any way to map ensemble gene ids like ENSG00000010404 ( iduronate 2-sulfatase) to Entrez Gene UIDs e.g "3423" ? ...
gene ensembl entrez e-utils written 14 days ago by mk110 • updated 14 days ago by genomax85k
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Comment: C: How long does a dbGaP controlled data access request take (US extramural)?
... Ok thanks, I updated the post to specify we are a US institution but not inside the NIH itself. ...
written 11 weeks ago by mk110
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How long does a dbGaP controlled data access request take (US extramural)?
... I just found out we need to submit a request through eRA to get access to the raw sequencing for a single TCGA cancer type. How long does this process usually take? ...
tcga written 11 weeks ago by mk110
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scater/scran workflow for batches recompute size factors after MNN?
... This question is in reference to the excellent tutorial posted [on bioconductor site][1] on batch correction using scran. Specifically there is a comment that reads: > Technically, we should have performed variance modelling and feature selection after calling multiBatchNorm(). This ensures th ...
R bioconductor scater scran written 14 months ago by mk110
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Comment: C: How to submit a genomics package with lots of data to CRAN
... Thanks @Satosh Anand. It looks like Dave Kleinschmidt has permanently hosted the data package in that example on github, since it can't be hosted in CRAN. I've done a bit of digging and found the following [here][1]: > Packages on which a CRAN package depends should be available from a mainstr ...
written 17 months ago by mk110

Latest awards to mk

Appreciated 13 months ago, created a post with more than 5 votes. For Mapping Ensembl Gene IDs with dot suffix
Popular Question 13 months ago, created a question with more than 1,000 views. For Linking patient survival to gene-set analysis
Popular Question 17 months ago, created a question with more than 1,000 views. For GDC API query to map HT-seq FPKM UUID to a Case UUID
Popular Question 18 months ago, created a question with more than 1,000 views. For GDC API query to map HT-seq FPKM UUID to a Case UUID
Popular Question 19 months ago, created a question with more than 1,000 views. For GDC API query to map HT-seq FPKM UUID to a Case UUID
Student 19 months ago, asked a question with at least 3 up-votes. For Mapping Ensembl Gene IDs with dot suffix
Scholar 2.4 years ago, created an answer that has been accepted. For A: Creation of cellDataSet in Monocle 2 wants undocumented AnnotatedDataFrame: assa

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