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Tutorial:
Read data file containing both counts and annotation into edgeR
rpkm
edgeR
featureCounts
6 months ago
Gordon Smyth
50k
17
votes
2
replies
8.7k
views
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
1.2k
views
Tutorial:
Online workshop "Working with ChatGPT in R" 2023-03-09
chatgpt
programming
12 months ago
Wolfgang Huber
★ 13k
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
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
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
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
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
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
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
0
replies
1.7k
views
Tutorial:
Reading csv file in minfi
minfi
infinium 450K
Tutorial
5.1 years ago
lalchungnungabt17
• 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
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
0
replies
2.1k
views
Tutorial:
Using Subversion to update /devel branch of Bioconductor package
subversion
bioc-devel
package development
usedevel
Tutorial
6.6 years ago
Bohdan Khomtchouk
▴ 10
2
votes
0
replies
3.8k
views
Tutorial:
BoF Bioc2017: Analyzing publicly available cancer genomics data from GTEx and TCGA with Bioconductor
public data
TCGA
GTEx
Tutorial
6.6 years ago
shepherl
3.8k
1
vote
0
replies
3.0k
views
Tutorial:
BoF Bioc2017: Infrastructure for efficient storage and processing of large-scale single-cell genomics data
single-cell
objectstorage
Tutorial
6.6 years ago
shepherl
3.8k
6
votes
1
reply
3.1k
views
Tutorial:
BoF "Writing papers in Rmarkdown, BiocStyle... (and books, posters)"
biocstyle
Rmarkdown
Tutorial
6.6 years ago
Wolfgang Huber
★ 13k
0
votes
2
replies
2.2k
views
Tutorial:
LEA won't run lfmm sequentially and independently on individual environmental variables when d set to 0
LEA
lfmm
Tutorial
updated 6.8 years ago by
eric.frichot
• 0 • written 6.8 years ago by
afreedman405
• 0
8
votes
4
replies
4.3k
views
Tutorial:
Epigenomics RoadMap Project files now accessible via AnnotationHub
AnnotationHub
Epigenomics
BigData
RoadMap Project
NIH
Tutorial
updated 6.9 years ago by
vanesa_1230
• 0 • written 8.8 years ago by
Sonali Arora
▴ 390
3
votes
8
replies
2.9k
views
Tutorial:
"developing" with HDF5Array
hdf5
DelayedArray
summarizedexperiment
Tutorial
7.1 years ago
Vincent J. Carey, Jr.
6.7k
0
votes
0
replies
7.4k
views
Tutorial:
doParallel foreach already exporting variable(s)
doParallel
foreach
export
Tutorial
7.1 years ago
solo7773
▴ 10
4
votes
0
replies
3.3k
views
Tutorial:
Workflow for low-level analysis of single-cell RNA-seq data
scran
scater
single cell
Tutorial
7.6 years ago
Aaron Lun
★ 28k
5
votes
1
reply
3.2k
views
Tutorial:
Prototyping An Analysis Pipeline For Lexogen 3'-UTR RNA-seq In Bioconductor
shortread
rsubread
ensembldb
Tutorial
7.9 years ago
phil.chapman
▴ 150
7
votes
0
replies
3.6k
views
Tutorial:
New edX "Data analysis for Life Sciences" module: High performance computing for reproducible genomics
annotation
genomicranges
visualization
docker
shiny
Tutorial
8.0 years ago
Vincent J. Carey, Jr.
6.7k
7
votes
2
replies
5.9k
views
Tutorial:
Course Material from BioC 2015: Where Software and Biology Connect
bioc2015
course-material
Tutorial
updated 8.7 years ago by
Dan Tenenbaum
★ 8.2k • written 8.7 years ago by
Sonali Arora
▴ 390
11
votes
0
replies
5.7k
views
Tutorial:
Introduction to Bioconductor for high-throughput sequence analysis
GenomicRanges
Annotation
RNAseq
visualization
Tutorial
8.7 years ago
Martin Morgan
25k
6
votes
1
reply
3.8k
views
Tutorial:
Orchestrating a small, parallel, RNA-seq pre-processing workflow using R
rnaseq
biocparallel
workflows
sra
Tutorial
8.7 years ago
Sean Davis
21k
8
votes
0
replies
3.5k
views
Tutorial:
Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq
chipseq
visualization
metagenomics
proteomics
Tutorial
8.7 years ago
Martin Morgan
25k
3
votes
0
replies
3.7k
views
Tutorial:
dplyr and the GEOmetadb package for mining NCBI GEO metadata
geometadb
dplyr
Tutorial
8.8 years ago
Sean Davis
21k
32 results • Page
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Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Votes
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: padj-based gradient scale from barplot (clusterProfiler results) does not work p
C: How to check that the reads in two fastq files are in the same order
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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