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Tutorial
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reset
6
votes
1
reply
2.9k
views
Tutorial:
Accessing Public Genomic Data from Bioconductor
geoquery
geometadb
sradb
Tutorial
updated 16 days ago by
Ruban Rex
• 0 • written 5.9 years ago by
Sean Davis
21k
1
vote
3
replies
100
views
Unable to reproduce Pasilla dataset which fresh instalation
tutorial
DESeq2
pasilla
9 weeks ago
Carina
• 0
3
votes
0
replies
231
views
Tutorial:
Mass Spectrometry Data Analysis with the Spectra Package
mass spectrometry
proteomics
metabolomics
Tutorial
6 months ago
Johannes Rainer
★ 1.9k
5
votes
4
replies
233
views
Comparing DEseq2 and Limma program, results not consistent
limma
deseq2
Tutorial
updated 6 months ago by
Gordon Smyth
42k • written 6 months ago by
yuemolinn
• 0
0
votes
1
reply
84
views
Can I apply tximport to transcript-level estimates obtained using cufflinks (cuffquant and cuffnorm) ??
tximport Cufflink
Tutorial
updated 6 months ago by
Kevin Blighe
2.8k • written 6 months ago by
LeiaMax2020
• 0
0
votes
1
reply
71
views
Differential expression analysis comparison using more that two variables
deseq2
Tutorial
updated 8 months ago by
Kevin Blighe
2.8k • written 8 months ago by
taniachavarria79
• 0
0
votes
2
replies
206
views
Warning messages: gseaKEGG
clusterProfiler
r
Tutorial
updated 8 months ago by
Kevin Blighe
2.8k • written 8 months ago by
Do it!
▴ 10
1
vote
2
replies
104
views
question for "Chapter 24 Zeisel mouse brain (STRT-Seq) in single-cell"
STRT-Seq
single-cell
tutorial
updated 10 months ago by
Aaron Lun
★ 26k • written 10 months ago by
tiphaine.martin
• 0
0
votes
1
reply
79
views
DESeq2 Experiment Setup
deseq2
Tutorial
updated 10 months ago by
Michael Love
32k • written 10 months ago by
Anna.bramucci
• 0
0
votes
0
replies
328
views
Tutorial:
[LIBD rstats club] Bioconductor overview
bioconductor
libdrstats
Tutorial
updated 11 months ago by
Laurent Gatto
1.5k • written 11 months ago by
Leonardo Collado Torres
▴ 870
1
vote
5
replies
175
views
ComplexHeatmap - R Session aborted after calling Heatmap()
software error
Tutorial
updated 11 months ago by
Zuguang Gu
▴ 210 • written 11 months ago by
AR3513
• 0
4
votes
0
replies
384
views
Tutorial:
How to post Salmon data to GEO for use with tximeta
salmon
tximeta
Tutorial
12 months ago
Michael Love
32k
0
votes
2
replies
99
views
Calculation of Log2 fold change in DEXSeq
DEXSeq
log2foldchange
Tutorial
updated 12 months ago by
Martin Morgan
25k • written 12 months ago by
tmvarsha
• 0
1
vote
2
replies
307
views
Tutorial:
selecting result from deseq2
deseq2
Tutorial
updated 12 months ago by
Michael Love
32k • written 12 months ago by
Nas 1989
• 0
1
vote
8
replies
470
views
BioMart: curl option when using getBM in loop
curl
biomart
getBM
Tutorial
updated 13 months ago by
James W. MacDonald
56k • written 13 months ago by
Ni-Ar
▴ 10
0
votes
2
replies
701
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 16 months ago by
Martin Morgan
25k • written 16 months ago by
crgarcia
• 0
4
votes
18
replies
3.0k
views
Batch correction by using ComBat function in sva package
deseq2
combat
Knownbatcheffect
Tutorial
updated 9 weeks ago by
Samuel Daniel
• 0 • written 18 months ago by
rajeshparmar4
• 0
0
votes
2
replies
136
views
Display number of downloads on a website
DMCHMM
Tutorial
updated 19 months ago by
shepherl
2.6k • written 19 months ago by
shokoohi
• 0
0
votes
1
reply
652
views
monocle error at orderCells
scRNA
monocle
packages
Tutorial
19 months ago
444579004
• 0
0
votes
5
replies
196
views
EnsemblGene ID conversion
deseq2
annotation
Tutorial
updated 20 months ago by
Martin Morgan
25k • written 20 months ago by
trumbia
• 0
0
votes
2
replies
2.0k
views
R Version 3.6.1
software error
Tutorial
updated 20 months ago by
Laurent Gatto
1.5k • written 20 months ago by
naeemurself
• 0
0
votes
0
replies
408
views
Tutorial:
Is there any R package for filtering out SNP markers?
annotation
Tutorial
21 months ago
prodhan82
▴ 10
0
votes
1
reply
492
views
Tutorial:
Differential Methylation Analysis using ChAMP
champ
Tutorial
updated 21 months ago by
Yuan Tian
▴ 220 • written 22 months ago by
learning.iq84
• 0
1
vote
3
replies
498
views
Error on zlib.h while installing esATAC on Ubutu
software error
esATAC
zlib.h
Ubuntu
Tutorial
updated 21 months ago by
Martin Morgan
25k • written 21 months ago by
vedbar
• 0
0
votes
7
replies
431
views
ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC
ATAC
ATACseq
software error
Tutorial
updated 22 months ago by
Steve Lianoglou
13k • written 22 months ago by
mbasam
• 0
0
votes
1
reply
563
views
How to change font size in ClusterProfiler
clusterProfiler
font size
Tutorial
updated 23 months ago by
Gordon Smyth
42k • written 23 months ago by
bony.dekumar
• 0
1
vote
1
reply
515
views
Tutorial:
How to download reference genomes using the RBioMart from ensembl?
BioMart
downloading reference genome
alignment
Tutorial
2.0 years ago
jcollidelcs
• 0
0
votes
4
replies
323
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 2.1 years ago by
Michael Love
32k • written 2.1 years ago by
wwu222
• 0
16
votes
1
reply
3.7k
views
Tutorial:
Updated Support Site Editor
support.bioconductor.org
editor
markdown
updates
Tutorial
updated 2.1 years ago by
lisaolley91
• 0 • written 2.2 years ago by
shepherl
2.6k
0
votes
0
replies
562
views
Tutorial:
Reading csv file in minfi
minfi
infinium 450K
Tutorial
2.2 years ago
lalchungnungabt17
• 0
5
votes
3
replies
358
views
Setting gene expression thresholds for trajectory analysis using Monocle
monocle
differential gene expression
detectgenes function
Tutorial
2.2 years ago
S.Webb6
▴ 40
0
votes
0
replies
492
views
How to extract SNPs from multiple alignment fasta file?
snp
multiple sequence alignment
fasta
Tutorial
updated 2.5 years ago by
Martin Morgan
25k • written 2.5 years ago by
pltbiotech_tkarthi
• 0
1
vote
2
replies
348
views
trouble importing data for DEseq2 workflow
deseq2
tximport
tximportdata
pasilla
Tutorial
updated 2.5 years ago by
Michael Love
32k • written 2.5 years ago by
Stanley Yang
• 0
2
votes
1
reply
399
views
GSVA tutorial brainTxDb oligodendrocytic_dn neuronal_dn are same genesets
GSVA
tutorial
updated 2.6 years ago by
Robert Castelo
★ 2.7k • written 2.6 years ago by
owen.whitley
• 0
1
vote
4
replies
635
views
EdgeR filtering, gene expression, cpm cutoff
edger
Tutorial
updated 2.7 years ago by
Hotz, Hans-Rudolf
▴ 400 • written 2.7 years ago by
ilovesuperheroes1993
• 0
2
votes
2
replies
413
views
Change legend names when using plotBCV
edger
plot
Tutorial
updated 2.7 years ago by
Gordon Smyth
42k • written 2.7 years ago by
Juan
• 0
0
votes
3
replies
629
views
running GEO series matrix file normalization and DEGs in limma
limma
normalization
Tutorial
updated 2.8 years ago by
James W. MacDonald
56k • written 2.8 years ago by
devarajsaranya
• 0
1
vote
0
replies
740
views
Tutorial:
Update gene symbols in GeneSetCollection
gseabase
msigdb
genesetcollection
Tutorial
2.8 years ago
t.kuilman
170
0
votes
4
replies
911
views
Tutorial:
Importing multiple .h5 files using tximport
tximport
Tutorial
updated 3.0 years ago by
Steve Lianoglou
13k • written 3.0 years ago by
nelson.s.garcia
▴ 10
0
votes
6
replies
940
views
Tutorial:
use deseq2 in asthma
deseq2
Tutorial
3.0 years ago
krwyaong.ju
• 0
1
vote
2
replies
583
views
Beta-matrix - Differential methylation analysis
ChAMP
tutorial
3.0 years ago
Dave Emir
• 0
1
vote
3
replies
559
views
Gene ID Duplicates
deseq2
genetics
Tutorial
updated 3.0 years ago by
James W. MacDonald
56k • written 3.0 years ago by
anokhi1997
• 0
20
votes
10
replies
6.0k
views
Tutorial:
Bioconductor on Coursera
mooc
Tutorial
updated 3.1 years ago by
ifmrdatascience
• 0 • written 5.6 years ago by
Kasper Daniel Hansen
6.5k
3
votes
5
replies
1.9k
views
Tutorial:
Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile
R
GEO
geoquery
geoquery error message
Tutorial
3.2 years ago
martinguerrerog89
▴ 20
0
votes
3
replies
559
views
How to install MethylKit?
methylkit
Tutorial
updated 3.4 years ago by
Martin Morgan
25k • written 3.4 years ago by
s1432985
• 0
0
votes
2
replies
512
views
normalizationFactors DESeq2 package
deseq2
Tutorial
updated 3.5 years ago by
Gordon Smyth
42k • written 3.5 years ago by
mariamari693693
• 0
4
votes
5
replies
682
views
SC3 gene clusters
SC3
single cell
single-cell
Tutorial
updated 3.5 years ago by
Martin Morgan
25k • written 3.5 years ago by
ahmed.elewa
▴ 20
0
votes
3
replies
885
views
Pathview -- Error in korg[ridx, coln] : subscript out of bounds
pathview
korg
subscript out of bounds
Tutorial
updated 3.6 years ago by
Luo Weijun
★ 1.5k • written 3.6 years ago by
aacevedo
• 0
0
votes
0
replies
1.1k
views
Tutorial:
Using Subversion to update /devel branch of Bioconductor package
subversion
bioc-devel
package development
usedevel
Tutorial
3.7 years ago
Bohdan Khomtchouk
▴ 10
2
votes
0
replies
2.0k
views
Tutorial:
BoF Bioc2017: Analyzing publicly available cancer genomics data from GTEx and TCGA with Bioconductor
public data
TCGA
GTEx
Tutorial
3.7 years ago
shepherl
2.6k
78 results • Page
1 of 2
Recent ...
Replies
Answer: unable to forge custom BSgenome after update
by
Hervé Pagès
14k
Hi, You need to specify the `circ_seqs` field in your seed file. `forgeBSgenomeDataPkg()` needs to know which sequences are circular …
Comment: How to apply limma-trend or voom to batch corrected single cell data? (non-integ
by
hainct
• 0
Thank you @alun
Comment: EnhancedVolcano plot with colCustom
by
Neeraja Vegesna
▴ 10
Hi Kevin, It worked once I added `names(keyvals.colour1)[keyvals.colour1 == '#8F8F8F'] <- 'NA'`. ![volcanoplot][1] Thanks a lot for you…
Comment: CUT&Tag differential peak analysis using Diffbind, with pre-calculated normaliza
by
mwong043
• 0
Thanks Rory. I tried the first method by defining a vector containing the normalisation factors for my samples and it worked. I am just wo…
Comment: EnhancedVolcano plot with colCustom
by
Kevin Blighe
2.8k
Hi, that's great that it works with a lower number of groups. Can you re-check the logic flow when you are using more groups? *EnhancedVolc…
Votes
mgcv not updating
Answer: How to apply limma-trend or voom to batch corrected single cell data? (non-integ
Answer: How to apply limma-trend or voom to batch corrected single cell data? (non-integ
Answer: How to apply limma-trend or voom to batch corrected single cell data? (non-integ
Comment: EnhancedVolcano plot with colCustom
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