notes from the birds of a feather session at the Bioconductor Developer Day 2017-07-26
## __Writing papers in Rmarkdown, BiocStyle... (and books, posters)__
__Multi-panel figures __
<span style="background-color:transparent
Order by: Relevance
Hello everyone! I am trying to annotate a list of regions as my regions are 502 bp long sometimes they overlap with more than 2 distinct genes , for example `chr2:112541661_112542162` overlaps with both POLR1B and LOC105373562 ( the first gene is on + strand and the latter is on - strand).
I am using `annotatePeak` function as follows:
txdb<- TxDb.Hsapiens.UCSC.hg38.knownGene
…
updated 4.4 years ago • pegah.taklifi
internally in memory...
FlatteningGtf: starting...(2021-02-16 17:38:56)
FlatteningGtf: gtf file read complete.(2021-02-16 17:40:24)
FlatteningGtf: Splice Junction Map read.(2021-02-16...17:40:26)
FlatteningGtf: gene Sets generated.(2021-02-16 17:40:28)
FlatteningGtf: Aggregate Sets built.
FlatteningGtf: Compiling Aggregate Info . . . (2021-02-16 1…
updated 4.8 years ago • n.tear
1.1.0 2016-07-27 [1] CRAN (R 4.0.0)
V cli 2.2.0 2021-01-31 [1] CRAN (R 4.0.2)
colorspace 2.0-0 2020-11-11 [1] CRAN (R 4.0.2)
V crayon 1.3.4 2021-02-08 [1] CRAN (R 4.0.3)
curl 4.3 2019-12-02 [1] CRAN...1.13.6 2020-12…
updated 4.8 years ago • hwu12
of Early Career Researchers committed to reducing entry barriers into bioinformatics. In June 2021, we are hosting a virtual conference that will bring together a diverse group of Early Career Researchers from across...our nomination form [https://forms.gle/cD71qbQ7rBbVkJ6V7][2]. Nominations close on the 15th February 2021.
We are striving to make the conference as inclusive as possible with spe…
updated 4.8 years ago • Matthew Ritchie
The Bioc2021 Committee is accepting applications for [Scholarships](https://docs.google.com/forms/d/e/1FAIpQLSeOE8FfcewYccR37o5dtC_tUjTCE5cKbyVMC_68uMuC3CgQbA/viewform) and [Caregiver](https://docs.google.com/forms/d/e/1FAIpQLSfumtkQAEllqZLF_dfHlGbIhELQojeu5uC9w7IO1rAOwgoj0w/viewform) awards. Please fill out the linked forms.
General information and registration can be obtained on the [conf…
updated 4.4 years ago • shepherl
fix this?
```r
> ref.data <- celldex::HumanPrimaryCellAtlasData(ensembl = T)
snapshotDate(): 2021-10-18
see ?celldex and browseVignettes('celldex') for documentation
loading from cache
see ?celldex and browseVignettes...celldex') for documentation
loading from cache
snapshotDate(): 2021-10-20
loading from cache
Error: failed to load resource
name: AH73881
title: Ensembl 97 Ens…
updated 4.1 years ago • immuno.dh
install.packages("BiocManager")
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
> BiocManager::install(version = "3.14")
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories...CRAN: https://mirrors.tongji.edu.cn/CRAN
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Installation paths not writeable, unable to update…
updated 3.9 years ago • Jiafy3999
CRAN: https://cran.rstudio.com/
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Old packages: 'Matrix'
Update all/some/none? [a/s/n]:
```
Matrix 1.4.0 is released in 2021/12/8. but in my environment, its compile
updated 4.0 years ago • 亮
the problem - (imkxpc_attributesForCharacterIndex:reply:) block performed very slowly (2.30 secs).
2021-02-05 21:13:11.213 R[48867:3744773] IMKClient Stall detected, *please Report* your user scenario attaching a spindump (or...the problem - (imkxpc_attributesForCharacterIndex:reply:) block performed very slowly (2.44 secs).
2021-02-05 21:13:14.387 R[48867:3744773] IMKClient Stall detected, *pl…
updated 4.8 years ago • xiaofeiwang18266
and evidence synthesis. By facilitating the creation of well-researched and professionally written papers, nurse paper writing services contribute to the advancement of nursing knowledge and practice.
One significant benefit...often require students to complete numerous research papers and projects, which can be challenging to manage alongside clinical placements and coursework. Nurse paper wr…
updated 19 months ago • pehisot636
2021-01-30 [1] Bioconductor
matrixStats * 1.3.0 2024-04-11 [1] CRAN (R 4.0.2)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.0.2)
mime 0.12 2021-09...purrr * 1.0.2 2023-08-10 [1] CRAN (R 4.0.2)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.0.2)
rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.0.2)
R…
Hi all,
In trying to perform a downstream analysis of human RNA-seq with WGCNA (with part of this [dataset][1]), I was trying to extract counts after importation of Salmon quants with `tximeta`. As I wanted to implement advice from this [paper][2] , my goal was to extract counts with minimal normalization, to then perform the upper quartile normalization recommanded in the aforementioned pape…
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit
updated 4.2 years ago • Fiona
ririzarr@jhsph.edu>,
"'Victor Markowitz (E-mail)'" <vmarkowitz@genelogic.com>
Subject: Call for Papers: 2003 Affymetrix GeneChip Microarray Low-
level An
alysis Workshop
2003 Affymetrix GeneChip Microarray Low-level
updated 22.6 years ago • Rafael A. Irizarry
mingw32 systems type 64-bit operating system, x64-based processor
status
major 4
minor 1.0
year 2021
month 05
day 18
svn rev 80317
language R
version.string R version 4.1.0 (2021-05-18)
nickname Camp Pontanezen
memory.limit
updated 4.3 years ago • Yoan
Dear List,
I am trying to duplicate the analysis using csaw in the paper, "From reads to regions", https://pubmed.ncbi.nlm.nih.gov/26834993/
I received different values than the paper for the...10088710 730440 94.07138 7.240172
```
Results for Mapped and Marked differ from the published paper.
```
indexBam(bam.files)
library(rtracklayer)
ch <- import.chain("mm9ToMm10.over.chain")
…
updated 4.6 years ago • richardallenfriedmanbrooklyn
install.packages("BiocManager")
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
>
> BiocManager::install("Biostrings")
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Warning
updated 3.7 years ago • lulucode
reported by the `getSQLiteFile()` function says that the version of the database is from Nov 3rd, 2021:
```r
> getSQLiteFile(destdir="/Users/robert")
trying URL 'https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz'
Content type...name value
1 schema version 1.0
2 creation timestamp 2021-11-03 01:18:38
[1] "/Users/robert/GEOmetadb.sqlite"
```
Would …
updated 2.8 years ago • Robert Castelo
div class="preformatted">
Hi All,
We'll be presenting a poster and then a paper for which I've performed
the
data analysis using R, Bioconductor, and the affy package. I want to
cite
both a paper (so the...can find the code!) for each.
I would appreciate some help getting the citations right.
For R:
======
Paper: (as recommended in the R FAQ)
------
R. Ihaka and R. Gentleman (1996), R: A…
<div class="preformatted">Dear All,
I am confussed about the differences between mergeLevels (in package
aCGH) and
MergeLevels.new (package snapCGH), and which one is the recommended
merging
procedure to use.
By the description in the help, mergeLevels (aCGH) is the one used in
the
Willenbrock & Fridlyand Bioinformatics 2005 paper. The defaults of
mergeLevels (Wilcoxon p-value, An…
not available for Bioconductor version '3.14'
```r
> sessionInfo( )
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)
Matrix products: default
locale...CRAN: https://cran.rstudio.com/
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Installing package(s) 'synapter'
Installatio…
deleted the Bioconductor package and reinstalled but this has not worked. I'm using a MacBook Pro M1 (2021).
I have no clue how to properly format a question on here so sorry if it doesn't make sense. But this is the code I have put in...CRAN: http://cran.rstudio.com/
```
```
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01)
Installing package(s) 'limma'
Package which is on…
updated 3.8 years ago • jaydengitt
div class="preformatted">I remember reading a paper on the discordance of microarray
measurements and
protein expression levels. Anybody can remind me what the paper
updated 9.8 years ago • Simon Lin
09) will be held from 14 to 16 August 2009, in
Tianjin,
China. We cordially invite you to submit a paper(s) and/or organize an
invited session. Due to numerous requests, the submission deadline is
extended to 10 March 2009...such as the Huangyaguan Great Wall,
Dule Temple, Panshan Mountain and Food Street.
Selected best papers will appear in SCI-indexed journal(s), such as
the Soft Computing jou…
updated 16.8 years ago • ICNC'09-FSKD'09
09) will be held from 14 to 16 August 2009, in
Tianjin,
China. We cordially invite you to submit a paper(s) and/or organize an
invited session. Due to numerous requests, the submission deadline is
extended to 10 March.
Tianjin...such as the Huangyaguan Great Wall,
Dule Temple, Panshan Mountain and Food Street.
Selected best papers will appear in SCI-indexed journal(s), such as
the Soft Computin…
updated 16.8 years ago • ICNC'09-FSKD'09
CRAN: https://cloud.r-project.org
Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Installing package(s) 'conumee'
installation de la dépendance ‘IlluminaHumanMethylationEPICanno.ilm10b2.hg19...installation of package ‘conumee’ had non-zero exit status
```
```
R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical …
updated 4.4 years ago • diego.bardiaux
div class="preformatted">I've been testing out the pamr package and have read the paper
"Diagnosis of multiple cancer types by shrunken centroids of gene
expression" by Tibshirani, et. al. In the paper it mentions...khan.txt
tutorial data I've tried setting nfold = 10 to ensure I can reproduce
the results from the paper. It still only does an 8-fold
cross-validation. Is this a bug or am I miss…
version 10.15.7).
The R version is:
Darwin Kernel Version 19.6.0: Mon Apr 12 20:57:45 PDT 2021; root:xnu-6153.141.28.1~1/RELEASE_X86_64
RStudio Version: 1.4.1106
.Renviron
R_LIBS=/Users/bc/RPackages
R_LIBS_SITE...bc/RPackages
##### Now, I start up RStudio and this is what happens. #####
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation fo…
updated 4.6 years ago • Joe
HiC data-sets, I was asked to look at the \`diffHiC\`. I read the user-manual and the paper. Congratulations on the paper. I have a question. The paper starts with reads or \`bam\` files. What if I already...help in this regard is highly appreciated.
What I have used is \`HiCPro\` (the first author of this paper also suggested that I us…
Hello,
I am trying to install 'phyloseq' and followed the instructions I found on the web. However, I did not successfully get 'phyloseq'
installed. I would be grateful for suggestions.
Thanks a lot,
Ina
> if (!requireNamespace("BiocManager", quietly = TRUE))
+ + install.packages("BiocManager")
> BiocManager::install("phyloseq")
Bioconductor version 3.1…
updated 4.4 years ago • Ina
A benchmarking paper (Geistlinger et.al 2020) recommended PADOG as one of the preferred tools for geneset analysis when you have an expression...dataset and have encountered a question about the output that I could not find an answer to in the paper, the vignette, or the GitHub issues.
The output contains the following:
1. ``meanAbsT0``: the mean of absolute t-scores
2. ``padog0...Given th…
updated 2.1 years ago • tim.meese
There's a duplicated word in the current limma userguide.pdf ('last revised 14 Nov 2021'), page 34:
```
(...)and Affymetrix arrays, include include con-
trol probes (...)
```
Btw this manual is a joy to read! Logical and clear, couldn
updated 3.1 years ago • jeltje.van.baren
Hope we could help you with all these fool proof guidelines to deliver successful **[Research paper help][1]**. Have these golden guidelines up your sleeves, and be ready to bag the highest grades in the class.
[1]: https://myassignmenthelp.com...nz/research-paper-help.html
updated 4.0 years ago • marryjamesus
<div class="preformatted">Hi,
I have been reading the papers "A Model Based Background Adjustment
for
Oligonucleotide Expression Arrays" and "Stochastic Models Inspired by
Hybridization...div class="preformatted">Hi,
I have been reading the papers "A Model Based Background Adjustment
for
Oligonucleotide Expression Arrays" and "Stochastic Models Inspired by...theory for short Oligonucleot…
<div class="preformatted">Dear list,
Some months ago, I read the following paper:
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/i2
82
It is said:"we identify a crucial step in GCRMA...div class="preformatted">Dear list,
Some months ago, I read the following paper:
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/i2
82
It is said:"we identify a c…
Dear BioC,
Could someone help , how to cite GCRMA and SAM?
Thank you so much in advance,
Saurin
Hi,
The comparison done in the "[functional enrichment for GTEx paper](http://guangchuangyu.github.io/2015/08/functional-enrichment-for-gtex-paper/)". I wonder if there is a way to do the
updated 8.9 years ago • fizer
to change it ( is it just an update on "DESCRIPTION" file and commit to git? )
The corresponding paper was just published 2 weeks agor, I also need to update the Bioconductor webpage with the correct citation info for the...paper. But I have no idea how
updated 8.7 years ago • ines.desantiago
value I should use for IQR filtering in
genefilter. I did some literature search. It varies from paper to
paper. I have read two papers so far. One used 0.5, the other used
0.18. affylmGUI has an option of 0.5, 0.25, and 0.1.
I also
Hello, I installed the latest R version 4.1.2, but now I got problem with installing the latest bioconductor version 3.14. Can anyone tell me what is going on? THANKS!
```
> if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
> BiocManager::install()
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for detai…
updated 4.0 years ago • array chip
packages but keep getting a message:
Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10)
Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.1.1/library
packages:
lattice
updated 4.2 years ago • Igor
https://forms.gle/d9PyAjAw62yVKxjL8) to nominate someone. The deadline for nominations is May 31, 2021
updated 4.5 years ago • shepherl
level quantifications to gene-level
gse = summarizeToGene(se)
loading existing EnsDb created: 2021-02-25 02:40:59
obtaining transcript-to-gene mapping from database
loading existing gene ranges created: 2021-02-25 02:52...a connection
# execute the command again
gse = summarizeToGene(se)
loading existing EnsDb created: 2021-02-25 02:40:59
obtaining transcript-to-gene mapping from database
loadin…
updated 4.5 years ago • Nikolay Ivanov
Given the formula from the paper/vignette for mu, I was expecting mu to be on a log normalized scale:
```
The mean values μ_ij = s_j * q_ij
where log2(q_ij) = X_j * B_i...48
```
What is the correct scale for mu?
```
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64
updated 3.8 years ago • chase.mateusiak
golubMerge (golubMerge.rda)
Combined Test and Training Sets from the Golub
Paper
golubTest (golubTest.rda)
Test Set Data from the Golub Paper
*golubTrain (golubTrain.rda)*
Training Set from the Golub...Paper
Thank you.
--
Gary Lipton
http://www.linkedin.com/in/garylipton
[[alternative HTML v…
updated 16.4 years ago • Gary Lipton
uname -a
Linux godfather 5.11.0-41-generic #45~20.04.1-Ubuntu SMP Wed Nov 10 10:20:10 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
manager@godfather:~$
```
Doing both:
```
manager@godfather:~$ R
R version 4.1.2 (2021-11-01) -- "Bird Hippie...Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY
updated 4.0 years ago • ALFONS
Hello All, as for 2021 is there a package that can read Affymetrix Axion SNP chips? I know there is an Axiom suite, but I am still waiting for my...Hello All, as for 2021 is there a package that can read Affymetrix Axion SNP chips? I know there is an Axiom suite, but I am still waiting for my IT
BiocManager::install("org.Mm.eg.db")
# Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.4 (2021-02-15)
# Installing package(s) 'org.Mm.eg.db'
# installing the source package ‘org.Mm.eg.db’
# 试开URL’https://bioconductor.org...Old packages: 'utf8'
# Update all/some/none? [a/s/n]:
# n
sessionInfo( )
# R version 4.0.4 (2021-02-15)
# Platform: x86_64-apple-darwin17.0 (64-bit)
# R…
updated 4.7 years ago • kevin
Hello
I find in this forum this link to a way to use clusterProfiler and TopGO to do GO and KO enrichment analysis form eggNOGmapper output (https://archetypalecology.wordpress.com/2021/01/27/how-to-perform-kegg-and-go-enrichment-analysis-of-non-model-species-using-r/) but it seems to be incomplete. Anyone know...do GO and KO enrichment analysis form eggNOGmapper output (https://archetypalecolog…
updated 2.2 years ago • nromerov
I have not been able to rsync from master.bioconductor.org since 04/18/2021. Are the rsync services purposely disabled or are they not available for some other reason at this time? Validated lack
https://forms.gle/d9PyAjAw62yVKxjL8) to nominate someone. The deadline for nominations is May 31, 2021
updated 4.6 years ago • shepherl
major 4
minor 0.5
year 2021
month 03
day 31
svn rev 80133
language R
version.string R version 4.0.5 (2021-03-31)
nickname Shake and Throw …
updated 4.1 years ago • AZ
gt; BiocManager::install("org.Hs.eg.db")
Bioconductor version 3.13 (BiocManager 1.30.15), R 4.1.0 (2021-05-18)
Installing package(s) 'org.Hs.eg.db'
installing the source package ‘org.Hs.eg.db’
trying URL 'https://bioconductor.org...include the results of running the following in an R session
sessionInfo( )
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running…
updated 4.5 years ago • chet.seligman
correct: the stamlab transcription factor binding motifs in
MotifDb are not from their 2012 Cell paper (pmid 22959076) but from
the Nature paper published at the same time (pmid 22955618):
"An expansive human regulatory lexicon...coming up
soon. I hope, too, to include all of the motif/TF gene mappings
alluded to in the paper:
A total of 394 of the 683 (58%) de novo motifs matched
di…
updated 11.8 years ago • Paul Shannon
I was reading https://www.cruk.cam.ac.uk/wp-content/uploads/2021/02/Quantitative-ChIPseq-Workshop-1.html, which mentions that "More complex schemes, such as forming a consensus peak
updated 19 months ago • Ian D.
Image Informatics in Biomedical Research and Clinical Medicine
ST12: e-Health
SUBMISSION GUIDELINES
Papers should be submitted electronically using EasyChair online
submission system. The papers must be prepared following...will be published by the IEEE Computer Society Press. At
least one of the authors of accepted papers is required to register
and present the work at the conference; otherwis…
updated 15.5 years ago • Amandeep Sidhu
Image Informatics in Biomedical Research and Clinical Medicine
ST12: e-Health
SUBMISSION GUIDELINES
Papers should be submitted electronically using EasyChair online
submission system. The papers must be prepared following...will be published by the IEEE Computer Society Press. At
least one of the authors of accepted papers is required to register
and present the work at the conference; otherwis…
updated 15.6 years ago • Amandeep Sidhu
I installed the latest R version 4.1.2, but I got problems with installing the latest bioconductor version 3.14. I can not install any package by bioconductor. Can anyone tell me the reason? THANKS!
```r
> if (!requireNamespace("BiocManager", quietly = TRUE))
+ install.packages("BiocManager")
>
> BiocManager::install("DESeq2")
'getOption("repos")' replaces Bioconductor …
updated 4.0 years ago • Evan
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes
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BTW, I tested with no issue on MacOS ARM on our previous github issue.
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The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup.
Maybe give the traceb…
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