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Tutorial:
Updated Support Site Editor
support.bioconductor.org
editor
markdown
updates
Tutorial
written 5.1 years ago by
shepherl
3.8k
0
votes
0
replies
444
views
News:
Include your Bioconductor tutorial in Smörgåsbord 2023, May 22-26!
Training
Bioconductor
Event
Community
Tutorial
10 months ago
Maria Doyle
▴ 70
1
vote
1
reply
993
views
Bioinformatics exercises for beginner
beginner
Bioconductor
tutorial
examples
updated 2.1 years ago by
Gordon Smyth
50k • written 2.1 years ago by
Sara
• 0
1
vote
1
reply
1.5k
views
Is there any R package for filtering out SNP markers?
Tutorial
annotation
updated 2.5 years ago by
Kevin Blighe
★ 3.9k • written 4.6 years ago by
prodhan82
▴ 20
7
votes
5
replies
6.0k
views
Tutorial:
Accessing Public Genomic Data from Bioconductor
geoquery
geometadb
sradb
Tutorial
written 8.8 years ago by
Sean Davis
21k
1
vote
3
replies
1.1k
views
Unable to reproduce Pasilla dataset which fresh instalation
tutorial
DESeq2
pasilla
3.1 years ago
Carina
• 0
3
votes
1
reply
2.1k
views
Tutorial:
Mass Spectrometry Data Analysis with the Spectra Package
mass spectrometry
proteomics
metabolomics
Tutorial
written 3.4 years ago by
Johannes Rainer
★ 2.0k
7
votes
4
replies
2.9k
views
Comparing DEseq2 and Limma program, results not consistent
limma
deseq2
Tutorial
updated 3.5 years ago by
Gordon Smyth
50k • written 3.5 years ago by
yuemolinn
• 0
0
votes
1
reply
878
views
Can I apply tximport to transcript-level estimates obtained using cufflinks (cuffquant and cuffnorm) ??
tximport Cufflink
Tutorial
updated 3.5 years ago by
Kevin Blighe
★ 3.9k • written 3.5 years ago by
LeiaMax2020
• 0
0
votes
1
reply
695
views
Differential expression analysis comparison using more that two variables
deseq2
Tutorial
updated 3.6 years ago by
Kevin Blighe
★ 3.9k • written 3.6 years ago by
taniachavarria79
• 0
0
votes
2
replies
1.2k
views
Warning messages: gseaKEGG
clusterProfiler
r
Tutorial
updated 3.6 years ago by
Kevin Blighe
★ 3.9k • written 3.6 years ago by
adR
▴ 30
1
vote
2
replies
856
views
question for "Chapter 24 Zeisel mouse brain (STRT-Seq) in single-cell"
STRT-Seq
single-cell
tutorial
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
tiphaine.martin
• 0
0
votes
1
reply
613
views
DESeq2 Experiment Setup
deseq2
Tutorial
updated 3.8 years ago by
Michael Love
41k • written 3.8 years ago by
Anna.bramucci
• 0
0
votes
0
replies
1.7k
views
Tutorial:
[LIBD rstats club] Bioconductor overview
bioconductor
libdrstats
Tutorial
updated 3.9 years ago by
Laurent Gatto
1.6k • written 3.9 years ago by
Leonardo Collado Torres
★ 1.0k
1
vote
5
replies
2.0k
views
ComplexHeatmap - R Session aborted after calling Heatmap()
software error
Tutorial
updated 3.9 years ago by
Zuguang Gu
▴ 240 • written 3.9 years ago by
AR3513
• 0
4
votes
0
replies
2.0k
views
Tutorial:
How to post Salmon data to GEO for use with tximeta
salmon
tximeta
Tutorial
3.9 years ago
Michael Love
41k
3
votes
3
replies
1.6k
views
Calculation of Log2 fold change in DEXSeq
DEXSeq
log2foldchange
Tutorial
updated 2.5 years ago by
rohitsatyam102
▴ 20 • written 4.0 years ago by
tmvarsha
▴ 20
1
vote
2
replies
1.9k
views
Tutorial:
selecting result from deseq2
deseq2
Tutorial
updated 4.0 years ago by
Michael Love
41k • written 4.0 years ago by
Nas 1989
• 0
1
vote
8
replies
8.7k
views
BioMart: curl option when using getBM in loop
curl
biomart
getBM
Tutorial
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
Ni-Ar
▴ 10
0
votes
2
replies
2.8k
views
Problems with bioconductor after updating R to 3.6.2
R 3.6.2 update problems with igraph and phangorn update
Phyloseq
igraph
phangorn
Tutorial
updated 4.2 years ago by
Martin Morgan
25k • written 4.2 years ago by
crgarcia
• 0
8
votes
18
replies
12k
views
Batch correction by using ComBat function in sva package
deseq2
combat
Knownbatcheffect
Tutorial
updated 3.1 years ago by
Samuel Daniel
• 0 • written 4.4 years ago by
rajeshparmar4
▴ 10
0
votes
2
replies
832
views
Display number of downloads on a website
DMCHMM
Tutorial
updated 4.5 years ago by
shepherl
3.8k • written 4.5 years ago by
shokoohi
• 0
0
votes
1
reply
4.5k
views
monocle error at orderCells
scRNA
monocle
packages
Tutorial
4.6 years ago
444579004
• 0
0
votes
5
replies
1.2k
views
EnsemblGene ID conversion
deseq2
annotation
Tutorial
updated 4.6 years ago by
Martin Morgan
25k • written 4.6 years ago by
trumbia
• 0
0
votes
2
replies
3.5k
views
R Version 3.6.1
software error
Tutorial
updated 4.6 years ago by
Laurent Gatto
1.6k • written 4.6 years ago by
naeemurself
• 0
0
votes
1
reply
2.1k
views
Tutorial:
Differential Methylation Analysis using ChAMP
champ
Tutorial
updated 4.7 years ago by
Yuan Tian
▴ 270 • written 4.8 years ago by
learning.iq84
• 0
1
vote
3
replies
1.8k
views
Error on zlib.h while installing esATAC on Ubutu
software error
esATAC
zlib.h
Ubuntu
Tutorial
updated 4.7 years ago by
Martin Morgan
25k • written 4.7 years ago by
vedbar
• 0
0
votes
7
replies
1.7k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC
ATAC
ATACseq
software error
Tutorial
updated 4.7 years ago by
Steve Lianoglou
★ 13k • written 4.7 years ago by
mbasam
• 0
0
votes
1
reply
1.8k
views
How to change font size in ClusterProfiler
clusterProfiler
font size
Tutorial
updated 4.9 years ago by
Gordon Smyth
50k • written 4.9 years ago by
bony.dekumar
• 0
1
vote
1
reply
1.9k
views
Tutorial:
How to download reference genomes using the RBioMart from ensembl?
BioMart
downloading reference genome
alignment
Tutorial
4.9 years ago
jcollidelcs
• 0
0
votes
4
replies
1.3k
views
How to analyze RNAseq data with multiple treatment groups and each subject has pre and post-treatment measures using deseq2/edger/limma?
deseq2
limma
edger
Tutorial
updated 5.0 years ago by
Michael Love
41k • written 5.0 years ago by
wwu222
• 0
0
votes
0
replies
1.7k
views
Tutorial:
Reading csv file in minfi
minfi
infinium 450K
Tutorial
5.1 years ago
lalchungnungabt17
• 0
5
votes
3
replies
1.3k
views
Setting gene expression thresholds for trajectory analysis using Monocle
monocle
differential gene expression
detectgenes function
Tutorial
5.1 years ago
S.Webb6
▴ 40
0
votes
0
replies
1.4k
views
How to extract SNPs from multiple alignment fasta file?
snp
multiple sequence alignment
fasta
Tutorial
updated 5.4 years ago by
Martin Morgan
25k • written 5.4 years ago by
pltbiotech_tkarthi
• 0
1
vote
2
replies
1.1k
views
trouble importing data for DEseq2 workflow
deseq2
tximport
tximportdata
pasilla
Tutorial
updated 5.4 years ago by
Michael Love
41k • written 5.4 years ago by
Stanley Yang
• 0
2
votes
1
reply
1.1k
views
GSVA tutorial brainTxDb oligodendrocytic_dn neuronal_dn are same genesets
GSVA
tutorial
updated 5.5 years ago by
Robert Castelo
★ 3.1k • written 5.5 years ago by
owen.whitley
▴ 10
1
vote
4
replies
2.5k
views
EdgeR filtering, gene expression, cpm cutoff
edger
Tutorial
updated 5.6 years ago by
Hotz, Hans-Rudolf
▴ 400 • written 5.6 years ago by
ilovesuperheroes1993
• 0
2
votes
2
replies
1.3k
views
Change legend names when using plotBCV
edger
plot
Tutorial
updated 5.6 years ago by
Gordon Smyth
50k • written 5.6 years ago by
Juan
• 0
0
votes
3
replies
1.4k
views
running GEO series matrix file normalization and DEGs in limma
limma
normalization
Tutorial
updated 5.7 years ago by
James W. MacDonald
65k • written 5.7 years ago by
devarajsaranya
• 0
1
vote
1
reply
1.9k
views
Tutorial:
Update gene symbols in GeneSetCollection
gseabase
msigdb
genesetcollection
Tutorial
written 5.7 years ago by
t.kuilman
▴ 170
0
votes
4
replies
3.2k
views
Tutorial:
Importing multiple .h5 files using tximport
tximport
Tutorial
updated 5.9 years ago by
Steve Lianoglou
★ 13k • written 5.9 years ago by
nelson.s.garcia
▴ 10
0
votes
6
replies
2.5k
views
Tutorial:
use deseq2 in asthma
deseq2
Tutorial
5.9 years ago
krwyaong.ju
• 0
1
vote
2
replies
2.2k
views
Beta-matrix - Differential methylation analysis
ChAMP
tutorial
5.9 years ago
Dave Emir
• 0
1
vote
3
replies
2.0k
views
Gene ID Duplicates
deseq2
genetics
Tutorial
updated 6.0 years ago by
James W. MacDonald
65k • written 6.0 years ago by
anokhi1997
• 0
21
votes
10
replies
8.5k
views
Tutorial:
Bioconductor on Coursera
mooc
Tutorial
updated 6.0 years ago by
ifmrdatascience
• 0 • written 8.5 years ago by
Kasper Daniel Hansen
★ 6.5k
3
votes
5
replies
4.8k
views
Tutorial:
Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile
R
GEO
geoquery
geoquery error message
Tutorial
6.2 years ago
martinguerrerog89
▴ 20
0
votes
3
replies
1.5k
views
How to install MethylKit?
methylkit
Tutorial
updated 6.3 years ago by
Martin Morgan
25k • written 6.3 years ago by
s1432985
• 0
0
votes
2
replies
1.3k
views
normalizationFactors DESeq2 package
deseq2
Tutorial
updated 6.4 years ago by
Gordon Smyth
50k • written 6.4 years ago by
mariamari693693
• 0
4
votes
5
replies
1.8k
views
SC3 gene clusters
SC3
single cell
single-cell
Tutorial
updated 6.4 years ago by
Martin Morgan
25k • written 6.4 years ago by
ahmed.elewa
▴ 20
0
votes
3
replies
2.2k
views
Pathview -- Error in korg[ridx, coln] : subscript out of bounds
pathview
korg
subscript out of bounds
Tutorial
updated 6.5 years ago by
Luo Weijun
★ 1.6k • written 6.5 years ago by
aacevedo
• 0
50 results • Page
1 of 1
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Replies
Comment: gds in GEOmetadb 2023-06-26 version is empty
by
ulna
• 0
[@ilayahari][1][basketball stars][2] The complete version of GEOmetadb cannot be downloaded, even though the demo file works. [1]: http…
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
If you include `0+` in the model formula, then the order of the batch and treatment factors in the model becomes important. You need `0+gro…
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
by
James W. MacDonald
65k
The main goal here is to map human gene symbols to something else, which you can use the `Orthology.eg.db` package to do. You could also us…
Comment: How can I compute AIC for MAST hurdle model fitted in the whole dataset?
by
rproendo
▴ 20
Hi OP, checking in to see if you found a solution to this issue. I'm also interested in using AICs to evaluate model fits in MAST.
Comment: padj-based gradient scale from barplot (clusterProfiler results) does not work p
by
Eva
▴ 10
Oh god, it is right, how I didn't realise before. I got confused with the scientific format of the numbers and I was in a loop for nothing.…
Votes
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
A: HLA genes missing from TxDb.Hsapiens.UCSC.hg38.knownGene
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
DESeq2 design with multiple factors
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