Admin: Martin Morgan

gravatar for Martin Morgan
Martin Morgan ♦♦ 23k
Reputation:
23,000
Status:
Trusted
Location:
United States
Website:
http://bioconductor.org/
Last seen:
4 hours ago
Joined:
13 years, 7 months ago
Email:
m************@gmail.com

Posts by Martin Morgan

<prev • 3,132 results • page 1 of 314 • next >
0
votes
1
answer
62
views
1
answers
Comment: C: Cannot down load the "org.Hs.eg.db" completely
... Please check disk space, both on the disk that the download file is located, and in the install location(s) indicated by `.libPaths()`. Is the library location (from `.libPaths()`) on a network share different from the temporary directory? ...
written 6 days ago by Martin Morgan ♦♦ 23k
0
votes
1
answer
62
views
1
answers
Answer: A: Cannot down load the "org.Hs.eg.db" completely
... ``` Warning messages: 1: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 331776 != reported length 2030028 ``` indicates that the download failed. Likely causes are an unreliable internet connection, disk full, or bad repository (hint for latter: don't set the option ...
written 6 days ago by Martin Morgan ♦♦ 23k
1
vote
1
answer
47
views
1
answers
Answer: A: Can't install the correct version of bioconductor, keeps using old version
... Is there a package 'BiocVersion' already installed, perhaps in /share/apps/rmodules? Use `"BiocVersion" %in% rownames(installed.packages())` If so, `remove.packages("BiocVersion")`, but probably this indicates that you're trying to re-use the R-3.5 library with R-3.6, which is generally not a good i ...
written 8 days ago by Martin Morgan ♦♦ 23k
0
votes
1
answer
30
views
1
answers
Answer: A: How can I import KEGG annotations
... `KEGGREST::keggGet()` might be helpful. ...
written 9 days ago by Martin Morgan ♦♦ 23k
0
votes
0
answers
77
views
0
answers
Comment: C: Error in installing bioconductor
... Likely the code is trying to execute the following line ``` config <- readLines("https://bioconductor.org/config.yaml") ``` and failing. What happens when you execute the line above? Please also provide the output of `sessionInfo()` in a new R session where the above line was attempted; here's mi ...
written 11 days ago by Martin Morgan ♦♦ 23k
1
vote
1
answer
49
views
1
answers
Comment: C: cn.mops on CRAM files
... if cn.mops uses Rsamtools, then unfortunately CRAM is not yet supported but this is very much a feature for this release cycle. ...
written 13 days ago by Martin Morgan ♦♦ 23k
1
vote
1
answer
54
views
1
answers
Answer: A: Can bioconductor package apply software copyright?
... If you intend to charge for commercial use, please choose a venue different from Bioconductor. ...
written 16 days ago by Martin Morgan ♦♦ 23k
0
votes
1
answer
61
views
1
answers
Comment: C: Mimic Counting of HTSeq-count Using countOverlaps
... Probably the easiest is to use the `ScanBamParam()` as the `param=` argument to `readGAlignments()` / `readGAlignmentPairs()`. Sorry about the NM / NH typo, corrected now. ...
written 19 days ago by Martin Morgan ♦♦ 23k
0
votes
0
answers
80
views
0
answers
Comment: C: summarizeOverlaps bplapply error in DeSeq2 pipeline
... It's a little confusing when you say 'still no luck', since you have been unlucky in three different ways (bplapply receive data failure; argument is not interpretable as logical; session aborted). Can you confirm that se <- summarizeOverlaps( features=ebg, reads=bamlist, mode="Unio ...
written 20 days ago by Martin Morgan ♦♦ 23k
2
votes
1
answer
61
views
1
answers
Answer: A: Mimic Counting of HTSeq-count Using countOverlaps
... The [STAR manual][1] says that alignments are unique when the NH tag is 1, or when the map quality is 255. One could use these in `ScanBamParam()`, e.g., `ScanBamParam(mapqFilter = 255)` or `ScanBamParam(tagFilter=list(NH = 1))` or `scanBamParam(mapqFilter = 255, tagFilter = list(NH = 1))`. The [HT ...
written 20 days ago by Martin Morgan ♦♦ 23k

Latest awards to Martin Morgan

Appreciated 6 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: Difficulty extending ExpressionSet
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: error with many packages: "Error : .onLoad failed in loadNamespace() for 'org.Hs
Scholar 8 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 8 months ago, created an answer that has been accepted. For A: Is BiocInstaller::biocLite incompatible with withr::with_makevars?
Teacher 8 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
Scholar 8 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Scholar 10 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Teacher 10 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
Popular Question 12 months ago, created a question with more than 1,000 views. For Updated Bioconductor Package Submission Policy
Scholar 12 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
Popular Question 12 months ago, created a question with more than 1,000 views. For BioC 2015 Annual Conference
Teacher 12 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 12 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
Scholar 12 months ago, created an answer that has been accepted. For A: How to get chip information from annotation databases
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: Error in GRanges: could not find symbol "recursive" in environment of the generi
Scholar 12 months ago, created an answer that has been accepted. For A: Difficulty extending ExpressionSet
Scholar 13 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
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Eliminating repetitive calls to ExperimentHub
Teacher 13 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
Scholar 13 months ago, created an answer that has been accepted. For A: How to get chip information from annotation databases
Scholar 24 months ago, created an answer that has been accepted. For A: about filtering variants in a VCF file

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 363 users visited in the last hour