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17
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Tutorial: Updated Support Site Editor
support.bioconductor.org editor markdown updates Tutorial
updated 5 weeks ago by • 0 • written 5.3 years ago by 3.9k
1
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1
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1.9k
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Tutorial: Update gene symbols in GeneSetCollection
gseabase msigdb genesetcollection Tutorial
written 5.9 years ago by ▴ 170
3
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1
reply
2.2k
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Tutorial: Mass Spectrometry Data Analysis with the Spectra Package
mass spectrometry proteomics metabolomics Tutorial
written 3.6 years ago by ★ 2.0k
0
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0
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498
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News: Include your Bioconductor tutorial in Smörgåsbord 2023, May 22-26!
Training Bioconductor Event Community Tutorial
12 months ago Maria Doyle ▴ 70
7
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5
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6.1k
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Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
written 8.9 years ago by 21k
1
vote
1
reply
1.1k
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Bioinformatics exercises for beginner
beginner Bioconductor tutorial examples
updated 2.2 years ago by 50k • written 2.2 years ago by • 0
1
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1
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1.5k
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Is there any R package for filtering out SNP markers?
Tutorial annotation
updated 2.6 years ago by ★ 3.9k • written 4.8 years ago by ▴ 20
3
votes
3
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1.7k
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Calculation of Log2 fold change in DEXSeq
DEXSeq log2foldchange Tutorial
updated 2.7 years ago by ▴ 20 • written 4.1 years ago by ▴ 20
8
votes
18
replies
12k
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Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 3.2 years ago by • 0 • written 4.6 years ago by ▴ 10
1
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3
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1.2k
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Unable to reproduce Pasilla dataset which fresh instalation
tutorial DESeq2 pasilla
3.2 years ago Carina • 0
7
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4
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3.1k
views
Comparing DEseq2 and Limma program, results not consistent
limma deseq2 Tutorial
updated 3.6 years ago by 50k • written 3.6 years ago by • 0
0
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1
reply
914
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Can I apply tximport to transcript-level estimates obtained using cufflinks (cuffquant and cuffnorm) ??
tximport Cufflink Tutorial
updated 3.6 years ago by ★ 3.9k • written 3.6 years ago by • 0
0
votes
1
reply
733
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Differential expression analysis comparison using more that two variables
deseq2 Tutorial
updated 3.7 years ago by ★ 3.9k • written 3.7 years ago by • 0
0
votes
2
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1.3k
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Warning messages: gseaKEGG
clusterProfiler r Tutorial
updated 3.7 years ago by ★ 3.9k • written 3.7 years ago by ▴ 30
1
vote
2
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913
views
question for "Chapter 24 Zeisel mouse brain (STRT-Seq) in single-cell"
STRT-Seq single-cell tutorial
updated 3.9 years ago by ★ 28k • written 3.9 years ago by • 0
0
votes
1
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649
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DESeq2 Experiment Setup
deseq2 Tutorial
updated 3.9 years ago by 41k • written 3.9 years ago by • 0
0
votes
0
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1.7k
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Tutorial: [LIBD rstats club] Bioconductor overview
bioconductor libdrstats Tutorial
updated 4.0 years ago by 1.6k • written 4.0 years ago by ★ 1.0k
1
vote
5
replies
2.1k
views
ComplexHeatmap - R Session aborted after calling Heatmap()
software error Tutorial
updated 4.0 years ago by ▴ 260 • written 4.0 years ago by • 0
4
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0
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2.1k
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Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
4.1 years ago Michael Love 41k
1
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2
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1.9k
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Tutorial: selecting result from deseq2
deseq2 Tutorial
updated 4.1 years ago by 41k • written 4.1 years ago by • 0
1
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8
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9.2k
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BioMart: curl option when using getBM in loop
curl biomart getBM Tutorial
updated 4.1 years ago by 65k • written 4.1 years ago by ▴ 10
0
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2
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2.9k
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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 4.4 years ago by 25k • written 4.4 years ago by • 0
0
votes
2
replies
870
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Display number of downloads on a website
DMCHMM Tutorial
updated 4.7 years ago by 3.9k • written 4.7 years ago by • 0
0
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1
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4.6k
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monocle error at orderCells
scRNA monocle packages Tutorial
4.7 years ago 444579004 • 0
0
votes
5
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1.2k
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EnsemblGene ID conversion
deseq2 annotation Tutorial
updated 4.7 years ago by 25k • written 4.7 years ago by • 0
0
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2
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3.5k
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R Version 3.6.1
software error Tutorial
updated 4.7 years ago by 1.6k • written 4.7 years ago by • 0
0
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1
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2.1k
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Tutorial: Differential Methylation Analysis using ChAMP
champ Tutorial
updated 4.8 years ago by ▴ 280 • written 4.9 years ago by • 0
1
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3
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1.9k
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Error on zlib.h while installing esATAC on Ubutu
software error esATAC zlib.h Ubuntu Tutorial
updated 4.8 years ago by 25k • written 4.8 years ago by • 0
0
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7
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1.8k
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ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 4.9 years ago by ★ 13k • written 4.9 years ago by • 0
0
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1
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1.8k
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How to change font size in ClusterProfiler
clusterProfiler font size Tutorial
updated 5.0 years ago by 50k • written 5.0 years ago by ▴ 10
1
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1
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2.0k
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Tutorial: How to download reference genomes using the RBioMart from ensembl?
BioMart downloading reference genome alignment Tutorial
5.0 years ago jcollidelcs • 0
0
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4
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1.4k
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 5.1 years ago by 41k • written 5.1 years ago by • 0
0
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0
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1.8k
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Tutorial: Reading csv file in minfi
minfi infinium 450K Tutorial
5.2 years ago lalchungnungabt17 • 0
5
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3
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1.4k
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Setting gene expression thresholds for trajectory analysis using Monocle
monocle differential gene expression detectgenes function Tutorial
5.3 years ago S.Webb6 ▴ 40
0
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0
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1.5k
views
How to extract SNPs from multiple alignment fasta file?
snp multiple sequence alignment fasta Tutorial
updated 5.6 years ago by 25k • written 5.6 years ago by • 0
1
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2
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1.2k
views
trouble importing data for DEseq2 workflow
deseq2 tximport tximportdata pasilla Tutorial
updated 5.6 years ago by 41k • written 5.6 years ago by • 0
2
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1
reply
1.2k
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GSVA tutorial brainTxDb oligodendrocytic_dn neuronal_dn are same genesets
GSVA tutorial
updated 5.6 years ago by ★ 3.3k • written 5.6 years ago by ▴ 10
1
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4
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2.6k
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EdgeR filtering, gene expression, cpm cutoff
edger Tutorial
updated 5.7 years ago by ▴ 400 • written 5.7 years ago by • 0
2
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2
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1.3k
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Change legend names when using plotBCV
edger plot Tutorial
updated 5.7 years ago by 50k • written 5.7 years ago by • 0
0
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3
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1.5k
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running GEO series matrix file normalization and DEGs in limma
limma normalization Tutorial
updated 5.8 years ago by 65k • written 5.8 years ago by • 0
0
votes
4
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3.3k
views
Tutorial: Importing multiple .h5 files using tximport
tximport Tutorial
updated 6.0 years ago by ★ 13k • written 6.0 years ago by ▴ 10
0
votes
6
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2.6k
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Tutorial: use deseq2 in asthma
deseq2 Tutorial
6.0 years ago krwyaong.ju • 0
1
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2
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2.4k
views
Beta-matrix - Differential methylation analysis
ChAMP tutorial
6.1 years ago Dave Emir • 0
1
vote
3
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2.1k
views
Gene ID Duplicates
deseq2 genetics Tutorial
updated 6.1 years ago by 65k • written 6.1 years ago by • 0
21
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10
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8.6k
views
Tutorial: Bioconductor on Coursera
mooc Tutorial
updated 6.1 years ago by • 0 • written 8.7 years ago by ★ 6.5k
3
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5
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5.0k
views
Tutorial: Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile
R GEO geoquery geoquery error message Tutorial
6.3 years ago martinguerrerog89 ▴ 20
0
votes
3
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1.6k
views
How to install MethylKit?
methylkit Tutorial
updated 6.4 years ago by 25k • written 6.4 years ago by • 0
0
votes
2
replies
1.4k
views
normalizationFactors DESeq2 package
deseq2 Tutorial
updated 6.5 years ago by 50k • written 6.5 years ago by • 0
4
votes
5
replies
1.8k
views
SC3 gene clusters
SC3 single cell single-cell Tutorial
updated 6.5 years ago by 25k • written 6.5 years ago by ▴ 20
0
votes
3
replies
2.3k
views
Pathview -- Error in korg[ridx, coln] : subscript out of bounds
pathview korg subscript out of bounds Tutorial
updated 6.6 years ago by ★ 1.6k • written 6.6 years ago by • 0
50 results • Page 1 of 1
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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