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17
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4
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9.8k
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Tutorial:
Updated Support Site Editor
support.bioconductor.org
editor
markdown
updates
Tutorial
updated 9 months ago by
Mj.A.
• 0 • written 5.9 years ago by
shepherl
4.1k
0
votes
0
replies
727
views
News:
Include your Bioconductor tutorial in Smörgåsbord 2023, May 22-26!
Training
Bioconductor
Event
Community
Tutorial
20 months ago
Maria Doyle
▴ 90
1
vote
1
reply
1.3k
views
Bioinformatics exercises for beginner
beginner
Bioconductor
tutorial
examples
updated 2.9 years ago by
Gordon Smyth
52k • written 2.9 years ago by
Sara
• 0
1
vote
1
reply
1.8k
views
Is there any R package for filtering out SNP markers?
Tutorial
annotation
updated 3.2 years ago by
Kevin Blighe
★ 4.0k • written 5.4 years ago by
prodhan82
▴ 20
7
votes
5
replies
6.7k
views
Tutorial:
Accessing Public Genomic Data from Bioconductor
geoquery
geometadb
sradb
Tutorial
written 9.6 years ago by
Sean Davis
21k
1
vote
3
replies
1.4k
views
Unable to reproduce Pasilla dataset which fresh instalation
tutorial
DESeq2
pasilla
3.9 years ago
Carina
• 0
3
votes
1
reply
2.8k
views
Tutorial:
Mass Spectrometry Data Analysis with the Spectra Package
mass spectrometry
proteomics
metabolomics
Tutorial
written 4.2 years ago by
Johannes Rainer
★ 2.1k
7
votes
4
replies
3.7k
views
Comparing DEseq2 and Limma program, results not consistent
limma
deseq2
Tutorial
updated 4.2 years ago by
Gordon Smyth
52k • written 4.2 years ago by
yuemolinn
• 0
0
votes
1
reply
1.1k
views
Can I apply tximport to transcript-level estimates obtained using cufflinks (cuffquant and cuffnorm) ??
tximport Cufflink
Tutorial
updated 4.2 years ago by
Kevin Blighe
★ 4.0k • written 4.2 years ago by
LeiaMax2020
• 0
0
votes
1
reply
883
views
Differential expression analysis comparison using more that two variables
deseq2
Tutorial
updated 4.3 years ago by
Kevin Blighe
★ 4.0k • written 4.3 years ago by
taniachavarria79
• 0
0
votes
2
replies
1.5k
views
Warning messages: gseaKEGG
clusterProfiler
r
Tutorial
updated 4.4 years ago by
Kevin Blighe
★ 4.0k • written 4.4 years ago by
adR
▴ 40
1
vote
2
replies
1.1k
views
question for "Chapter 24 Zeisel mouse brain (STRT-Seq) in single-cell"
STRT-Seq
single-cell
tutorial
updated 4.5 years ago by
Aaron Lun
★ 28k • written 4.5 years ago by
tiphaine.martin
• 0
0
votes
1
reply
786
views
DESeq2 Experiment Setup
deseq2
Tutorial
updated 4.6 years ago by
Michael Love
43k • written 4.6 years ago by
Anna.bramucci
• 0
0
votes
0
replies
2.1k
views
Tutorial:
[LIBD rstats club] Bioconductor overview
bioconductor
libdrstats
Tutorial
updated 4.6 years ago by
Laurent Gatto
1.6k • written 4.6 years ago by
Leonardo Collado Torres
★ 1.1k
1
vote
5
replies
2.6k
views
ComplexHeatmap - R Session aborted after calling Heatmap()
software error
Tutorial
updated 4.6 years ago by
Zuguang Gu
▴ 290 • written 4.6 years ago by
AR3513
• 0
4
votes
0
replies
2.4k
views
Tutorial:
How to post Salmon data to GEO for use with tximeta
salmon
tximeta
Tutorial
4.7 years ago
Michael Love
43k
3
votes
3
replies
2.1k
views
Calculation of Log2 fold change in DEXSeq
DEXSeq
log2foldchange
Tutorial
updated 3.3 years ago by
rohitsatyam102
▴ 20 • written 4.7 years ago by
tmvarsha
▴ 20
1
vote
2
replies
2.4k
views
Tutorial:
selecting result from deseq2
deseq2
Tutorial
updated 4.7 years ago by
Michael Love
43k • written 4.7 years ago by
Nas 1989
• 0
1
vote
8
replies
11k
views
BioMart: curl option when using getBM in loop
curl
biomart
getBM
Tutorial
updated 4.8 years ago by
James W. MacDonald
67k • written 4.8 years ago by
Ni-Ar
▴ 10
0
votes
2
replies
3.3k
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 5.0 years ago by
Martin Morgan
25k • written 5.0 years ago by
crgarcia
• 0
8
votes
18
replies
14k
views
Batch correction by using ComBat function in sva package
deseq2
combat
Knownbatcheffect
Tutorial
updated 3.8 years ago by
Samuel Daniel
• 0 • written 5.2 years ago by
rajeshparmar4
▴ 10
0
votes
2
replies
1.0k
views
Display number of downloads on a website
DMCHMM
Tutorial
updated 5.3 years ago by
shepherl
4.1k • written 5.3 years ago by
shokoohi
• 0
0
votes
1
reply
5.3k
views
monocle error at orderCells
scRNA
monocle
packages
Tutorial
5.3 years ago
444579004
• 0
0
votes
5
replies
1.5k
views
EnsemblGene ID conversion
deseq2
annotation
Tutorial
updated 5.4 years ago by
Martin Morgan
25k • written 5.4 years ago by
trumbia
• 0
0
votes
2
replies
3.8k
views
R Version 3.6.1
software error
Tutorial
updated 5.4 years ago by
Laurent Gatto
1.6k • written 5.4 years ago by
naeemurself
• 0
0
votes
1
reply
2.6k
views
Tutorial:
Differential Methylation Analysis using ChAMP
champ
Tutorial
updated 5.5 years ago by
Yuan Tian
▴ 290 • written 5.5 years ago by
learning.iq84
• 0
1
vote
3
replies
2.1k
views
Error on zlib.h while installing esATAC on Ubutu
software error
esATAC
zlib.h
Ubuntu
Tutorial
updated 5.5 years ago by
Martin Morgan
25k • written 5.5 years ago by
vedbar
• 0
0
votes
7
replies
2.1k
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC
ATAC
ATACseq
software error
Tutorial
updated 5.5 years ago by
Steve Lianoglou
★ 13k • written 5.5 years ago by
mbasam
• 0
0
votes
1
reply
2.3k
views
How to change font size in ClusterProfiler
clusterProfiler
font size
Tutorial
updated 5.6 years ago by
Gordon Smyth
52k • written 5.6 years ago by
bony.dekumar
▴ 10
1
vote
1
reply
2.5k
views
Tutorial:
How to download reference genomes using the RBioMart from ensembl?
BioMart
downloading reference genome
alignment
Tutorial
5.7 years ago
jcollidelcs
• 0
0
votes
4
replies
1.8k
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 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
wwu222
• 0
0
votes
0
replies
2.3k
views
Tutorial:
Reading csv file in minfi
minfi
infinium 450K
Tutorial
5.8 years ago
lalchungnungabt17
• 0
5
votes
3
replies
1.7k
views
Setting gene expression thresholds for trajectory analysis using Monocle
monocle
differential gene expression
detectgenes function
Tutorial
5.9 years ago
S.Webb6
▴ 40
0
votes
0
replies
1.7k
views
How to extract SNPs from multiple alignment fasta file?
snp
multiple sequence alignment
fasta
Tutorial
updated 6.2 years ago by
Martin Morgan
25k • written 6.2 years ago by
pltbiotech_tkarthi
• 0
1
vote
2
replies
1.3k
views
trouble importing data for DEseq2 workflow
deseq2
tximport
tximportdata
pasilla
Tutorial
updated 6.2 years ago by
Michael Love
43k • written 6.2 years ago by
Stanley Yang
• 0
2
votes
1
reply
1.3k
views
GSVA tutorial brainTxDb oligodendrocytic_dn neuronal_dn are same genesets
GSVA
tutorial
updated 6.3 years ago by
Robert Castelo
★ 3.4k • written 6.3 years ago by
owen.whitley
▴ 10
1
vote
4
replies
3.2k
views
EdgeR filtering, gene expression, cpm cutoff
edger
Tutorial
updated 6.3 years ago by
Hotz, Hans-Rudolf
▴ 400 • written 6.3 years ago by
ilovesuperheroes1993
• 0
2
votes
2
replies
1.5k
views
Change legend names when using plotBCV
edger
plot
Tutorial
updated 6.4 years ago by
Gordon Smyth
52k • written 6.4 years ago by
Juan
• 0
0
votes
3
replies
1.7k
views
running GEO series matrix file normalization and DEGs in limma
limma
normalization
Tutorial
updated 6.4 years ago by
James W. MacDonald
67k • written 6.5 years ago by
devarajsaranya
• 0
1
vote
1
reply
2.2k
views
Tutorial:
Update gene symbols in GeneSetCollection
gseabase
msigdb
genesetcollection
Tutorial
written 6.5 years ago by
t.kuilman
▴ 170
0
votes
4
replies
3.8k
views
Tutorial:
Importing multiple .h5 files using tximport
tximport
Tutorial
updated 6.6 years ago by
Steve Lianoglou
★ 13k • written 6.6 years ago by
nelson.s.garcia
▴ 10
0
votes
6
replies
3.0k
views
Tutorial:
use deseq2 in asthma
deseq2
Tutorial
6.7 years ago
krwyaong.ju
• 0
1
vote
2
replies
2.8k
views
Beta-matrix - Differential methylation analysis
ChAMP
tutorial
6.7 years ago
Dave Emir
• 0
1
vote
3
replies
2.3k
views
Gene ID Duplicates
deseq2
genetics
Tutorial
updated 6.7 years ago by
James W. MacDonald
67k • written 6.7 years ago by
anokhi1997
• 0
21
votes
10
replies
9.3k
views
Tutorial:
Bioconductor on Coursera
mooc
Tutorial
updated 6.8 years ago by
ifmrdatascience
• 0 • written 9.3 years ago by
Kasper Daniel Hansen
★ 6.5k
3
votes
5
replies
5.7k
views
Tutorial:
Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile
R
GEO
geoquery
geoquery error message
Tutorial
6.9 years ago
martinguerrerog89
▴ 20
0
votes
3
replies
1.9k
views
How to install MethylKit?
methylkit
Tutorial
updated 7.1 years ago by
Martin Morgan
25k • written 7.1 years ago by
s1432985
• 0
0
votes
2
replies
1.6k
views
normalizationFactors DESeq2 package
deseq2
Tutorial
updated 7.1 years ago by
Gordon Smyth
52k • written 7.1 years ago by
mariamari693693
• 0
4
votes
5
replies
2.1k
views
SC3 gene clusters
SC3
single cell
single-cell
Tutorial
updated 7.2 years ago by
Martin Morgan
25k • written 7.2 years ago by
ahmed.elewa
▴ 20
0
votes
3
replies
2.7k
views
Pathview -- Error in korg[ridx, coln] : subscript out of bounds
pathview
korg
subscript out of bounds
Tutorial
updated 7.2 years ago by
Luo Weijun
★ 1.6k • written 7.3 years ago by
aacevedo
• 0
50 results • Page
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Comment: Cross-validation with multiple control subgroups in limma
by
Ali Barry
▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma
by
Gordon Smyth
52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS
by
Aidan
▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
by
Michael Love
43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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