Admin: Martin Morgan

gravatar for Martin Morgan
Martin Morgan ♦♦ 23k
Reputation:
23,220
Status:
Trusted
Location:
United States
Website:
http://bioconductor.org/
Last seen:
7 hours ago
Joined:
13 years, 9 months ago
Email:
m************@gmail.com

Posts by Martin Morgan

<prev • 3,192 results • page 1 of 320 • next >
0
votes
1
answer
23
views
1
answers
Answer: A: package DESeqDataSet is not available for R version 3.6.1
... Do you mean to `BiocManager::install("DESeq2")` instead of `DEseqDataSet` (which has never existed, I think?). ...
written 7 hours ago by Martin Morgan ♦♦ 23k
0
votes
2
answers
51
views
2
answers
Answer: A: Is magrittr "%>%" acceptable in bioc packages?
... The complaint is about a missing `\value{}` section, which in roxygen-speak is a missing `@return` tag in the documentation chunk that creates the 'pipe.Rd' man page. ...
written 4 days ago by Martin Morgan ♦♦ 23k
0
votes
1
answer
41
views
1
answers
Answer: A: org.Hs.eg.db can not be downloaded
... The error message says 'load faild for 'AnnotationDbi'. Try loading it only ``` library(AnnotationDbi) ``` and try to understand the error it reports... ...
written 7 days ago by Martin Morgan ♦♦ 23k
0
votes
0
answers
94
views
0
answers
Comment: C: Error: se does not inherit from class SummarizedExperiment
... From the documentation `?test_diff` and Arne's answer, it seems like your object `data_imp_knn` should be a SummarizedExperiment, i.e., `is(data_imp_knn, "SummarizedExperiment")` should return TRUE. Does it? ...
written 16 days ago by Martin Morgan ♦♦ 23k
1
vote
0
answers
94
views
0
answers
Comment: C: Error: se does not inherit from class SummarizedExperiment
... For installation problems, be sure that you are in a new R session with no other R sessions running. Use the command `BiocManager::valid()` to check that you have a consistent installation. It looks like you're trying to use a 'devel' version of DEP (the odd number, '.7' in the version) and you're ...
written 18 days ago by Martin Morgan ♦♦ 23k
3
votes
1
answer
71
views
1
answers
Answer: A: flowWorkspace cannot load external data
... Based on this line ``` flowDataPath <- system.file("extdata", package = "flowWorkspaceData") ``` I'd guess that you would also need `BiocManager::install("flowWorkspaceData")` ...
written 19 days ago by Martin Morgan ♦♦ 23k
0
votes
1
answer
89
views
1
answers
Comment: C: Interpretation of the heatmap produced by DESeq2
... It's 'fun' to note that the notion of 'alphabetical' order depends on the locale, for instance in Estonian apparently 'z' sorts before 't' https://www.unicode.org/cldr/charts/30/collation/et.html so in my locale ``` > levels(factor(c("zero", "three"))) [1] "three" "zero" ``` whereas a user with a ...
written 19 days ago by Martin Morgan ♦♦ 23k
3
votes
2
answers
78
views
2
answers
Answer: A: the coordinates of exons of RefSeq or ENSEMBL genes
... For ensembl, load the ensembldb and AnnotationHub and query for EnsDb objects for Homo sapiens, release 97 > library(ensembldb) > library(AnnotationHub) > hub = AnnotationHub() snapshotDate(): 2019-07-10 > query(hub, c("EnsDb", "Homo sapiens", "97")) This returns a ...
written 19 days ago by Martin Morgan ♦♦ 23k
0
votes
1
answer
169
views
1
answers
Comment: C: Issue installing RNA-seq workflow
... It seems like your linux-based AWS environment needs something like lzma-dev system dependency to be installed, using apt get or similar depending on the operating system. ...
written 21 days ago by Martin Morgan ♦♦ 23k
0
votes
1
answer
55
views
1
answers
Answer: A: package 'hgu95av2.db' is not available (for R version 3.6.0)
... Install the package using standard Bioconductor installation instructions BiocManager::install("hgu95av2.db") ...
written 22 days ago by Martin Morgan ♦♦ 23k

Latest awards to Martin Morgan

Scholar 18 days ago, created an answer that has been accepted. For A: GSEABase: how to extract shortDescription from GeneSetCollection object
Teacher 18 days ago, created an answer with at least 3 up-votes. For A: how does coverage() works
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: how does coverage() works
Scholar 19 days ago, created an answer that has been accepted. For A: GSEABase: how to extract shortDescription from GeneSetCollection object
Scholar 7 months ago, created an answer that has been accepted. For A: bplapply with ShortRead functions
Popular Question 7 months ago, created a question with more than 1,000 views. For BioC 2017: Where Software and Biology Connect, 26 / 27 - 28 July, Boston, MA
Appreciated 7 months ago, created a post with more than 5 votes. For Bioconductor Technical Advisory Board
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Rsamtools use for R version 3.4.1
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: error with many packages: "Error : .onLoad failed in loadNamespace() for 'org.Hs
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: RSVSim insertions from chr1 to chr2
Scholar 7 months ago, created an answer that has been accepted. For A: error with many packages: "Error : .onLoad failed in loadNamespace() for 'org.Hs
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Best alternative annotation package to BiomaRt
Popular Question 7 months ago, created a question with more than 1,000 views. For Bioconductor Senior Programmer / Analyst
Scholar 7 months ago, created an answer that has been accepted. For A: How to get chip information from annotation databases
Scholar 7 months ago, created an answer that has been accepted. For A: Ranges from a fasta file
Scholar 7 months ago, created an answer that has been accepted. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Scholar 7 months ago, created an answer that has been accepted. For A: how does coverage() works
Scholar 7 months ago, created an answer that has been accepted. For A: DataFrame after splitting and back
Scholar 7 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Appreciated 7 months ago, created a post with more than 5 votes. For Statistics and Computing in Genome Science (CSAMA) Course Material
Scholar 7 months ago, created an answer that has been accepted. For A: GSEABase: how to extract shortDescription from GeneSetCollection object
Scholar 7 months ago, created an answer that has been accepted. For A: Is BiocInstaller::biocLite incompatible with withr::with_makevars?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Q score filter: 90% of the q scores from a QualityScaledDNAStringSet are above 3
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: how does coverage() works

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 249 users visited in the last hour