User: Yue Li

gravatar for Yue Li
Yue Li370
Reputation:
370
Status:
Trusted
Location:
USA
Website:
http://people.csail.mi...
Last seen:
3 years, 8 months ago
Joined:
7 years, 5 months ago
Email:
g*********@gmail.com

Posts by Yue Li

<prev • 36 results • page 2 of 4 • next >
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lower.limits and upper.limits in glmnet
... Dear List, A quick question about using the glmnet package (which I know is not a BioC package ... apologies): Would the options "upper.limits" and "lower.limits" in glmnet be equivalent to an additionally constrained optimization on the range of the coefficients? For instance, would setting uppe ...
regression written 6.0 years ago by Yue Li370 • updated 6.0 years ago by Yue Li60
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Find TF ID for a target gene ID
... Dear List, I wonder if anyone knows how to efficiently find TF IDs corresponding to a target gene ID (e.g., Ensembl) using packages such as biomaRt? Thanks much in advance, Yue ...
written 7.0 years ago by Yue Li370 • updated 6.9 years ago by Marc Carlson7.2k
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submission of new package
... Dear Bioconductor colleagues, I have a question regarding to the new package submission associated with a peer-review manuscript to some journal. The way I understand is that I first submit my package to Dr. Marc Carlson for review. Meanwhile, I could submit my manuscript describing the algorithm ...
written 7.1 years ago by Yue Li370 • updated 7.1 years ago by Yue Li60
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Comment: C: how to build a R package with the inclusion of inst/extdata
... Thanks Martin. I got it to work somehow by following the exactly the same workflow ... the file size is about 80 Mb but it manages to squeeze them into the tar ball eventually. On 2012-09-07, at 1:02 AM, Martin Morgan wrote: > On 09/06/2012 06:25 PM, Yue Li wrote: >> Sorry Steve, I'm a ...
written 7.1 years ago by Yue Li370
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Comment: C: how to build a R package with the inclusion of inst/extdata
... Sorry Steve, I'm actually stuck at building the package with inst/extdata. This is my first time trying to build a R package, so please bear with me. Let me walk you through my (incorrect) approach: I have a set of R scripts and Rd files that need to be built into a package. I deliberately make all ...
written 7.1 years ago by Yue Li370
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Comment: C: how to build a R package with the inclusion of inst/extdata
... Hi Steven, Thanks for the quick response. I think I probably didn't articulate my intend clearly. Basically, I'm trying to develop a R package rather than using someone else's package. In order to run some examples I have for the functions I wrote, I need to have BAM data saved in the "inst/extdat ...
written 7.1 years ago by Yue Li370
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how to build a R package with the inclusion of inst/extdata
... Dear list, I wonder if anyone could hint me on how to build a R package with the inclusion of "inst/extdata". Basically, I'm trying to build a R package with some BAM files as my test data used in the examples session from the Rd files. If I simply go: package.skeleton(name="myPackage", code_file ...
written 7.1 years ago by Yue Li370 • updated 7.1 years ago by Steve Lianoglou12k
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how to load RangedData for all chromosomes in one tab in UCSC browser using browserView from rtracklayer
... Not sure if you were asking a question or implying that it's not feasible with UCSC browser. Anyhow, I could just upload to UCSC the bed/bam/bedGraph/gff file containing ranges for multiple chromosomes. Then go to the browser-view to visualize any chromosome in a single window with my browser? On ...
go cancer rtracklayer written 7.4 years ago by Yue Li370 • updated 7.4 years ago by Steve Lianoglou12k
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how to load RangedData for all chromosomes in one tab in UCSC browser using browserView from rtracklayer
... Dear List, I wonder how to load RangedData for all chromosomes in a SINGLE tab in UCSC browser using browserView from rtracklayer. Currently, if I have a GRanges object for "mm9" build: > alignGR GRanges with 238161 ranges and 0 elementMetadata cols: seqnames ...
rtracklayer written 7.4 years ago by Yue Li370 • updated 7.4 years ago by Steve Lianoglou12k
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suppressMessages does not work with endoapply?
... Dear List, As the title states, I'm wondering whether there is a way to suppress all messages from function that is executed via endoapply. Currently, suppressMessages works with lapply but not endoapply. Thanks much, Yue ...
written 7.4 years ago by Yue Li370 • updated 7.4 years ago by Martin Morgan ♦♦ 23k

Latest awards to Yue Li

Popular Question 3.7 years ago, created a question with more than 1,000 views. For fail to load BSgenome.Hsapiens.UCSC.hg19
Popular Question 3.7 years ago, created a question with more than 1,000 views. For how to build a R package with the inclusion of inst/extdata
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Algorithm description for matchPWM (Biostrings)
Popular Question 3.7 years ago, created a question with more than 1,000 views. For lower.limits and upper.limits in glmnet
Student 3.7 years ago, asked a question with at least 3 up-votes. For Algorithm description for matchPWM (Biostrings)
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Algorithm description for matchPWM (Biostrings)

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