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Tutorial: Updated Support Site Editor
support.bioconductor.org editor markdown updates Tutorial
written 4.8 years ago by 3.6k
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News: Include your Bioconductor tutorial in Smörgåsbord 2023, May 22-26!
Training Bioconductor Event Community Tutorial
7 months ago Maria Doyle ▴ 50
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892
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Bioinformatics exercises for beginner
beginner Bioconductor tutorial examples
updated 21 months ago by 48k • written 21 months ago by • 0
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1.4k
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Is there any R package for filtering out SNP markers?
Tutorial annotation
updated 2.2 years ago by 3.9k • written 4.3 years ago by ▴ 20
7
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Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
written 8.5 years ago by 21k
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3
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977
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Unable to reproduce Pasilla dataset which fresh instalation
tutorial DESeq2 pasilla
2.8 years ago Carina • 0
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Tutorial: Mass Spectrometry Data Analysis with the Spectra Package
mass spectrometry proteomics metabolomics Tutorial
3.1 years ago Johannes Rainer ★ 2.0k
7
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4
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Comparing DEseq2 and Limma program, results not consistent
limma deseq2 Tutorial
updated 3.2 years ago by 48k • written 3.2 years ago by • 0
0
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781
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Can I apply tximport to transcript-level estimates obtained using cufflinks (cuffquant and cuffnorm) ??
tximport Cufflink Tutorial
updated 3.2 years ago by 3.9k • written 3.2 years ago by • 0
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617
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Differential expression analysis comparison using more that two variables
deseq2 Tutorial
updated 3.3 years ago by 3.9k • written 3.3 years ago by • 0
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2
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1.1k
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Warning messages: gseaKEGG
clusterProfiler r Tutorial
updated 3.3 years ago by 3.9k • written 3.3 years ago by ▴ 30
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757
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question for "Chapter 24 Zeisel mouse brain (STRT-Seq) in single-cell"
STRT-Seq single-cell tutorial
updated 3.4 years ago by ★ 28k • written 3.4 years ago by • 0
0
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545
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DESeq2 Experiment Setup
deseq2 Tutorial
updated 3.5 years ago by 41k • written 3.5 years ago by • 0
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Tutorial: [LIBD rstats club] Bioconductor overview
bioconductor libdrstats Tutorial
updated 3.6 years ago by 1.6k • written 3.6 years ago by ★ 1.0k
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ComplexHeatmap - R Session aborted after calling Heatmap()
software error Tutorial
updated 3.6 years ago by ▴ 240 • written 3.6 years ago by • 0
4
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Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
3.6 years ago Michael Love 41k
3
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3
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1.4k
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Calculation of Log2 fold change in DEXSeq
DEXSeq log2foldchange Tutorial
updated 2.2 years ago by ▴ 20 • written 3.7 years ago by ▴ 20
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1.7k
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Tutorial: selecting result from deseq2
deseq2 Tutorial
updated 3.7 years ago by 41k • written 3.7 years ago by • 0
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8
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BioMart: curl option when using getBM in loop
curl biomart getBM Tutorial
updated 3.7 years ago by 64k • written 3.7 years ago by ▴ 10
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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 3.9 years ago by 25k • written 3.9 years ago by • 0
8
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Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 2.8 years ago by • 0 • written 4.1 years ago by ▴ 10
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2
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741
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Display number of downloads on a website
DMCHMM Tutorial
updated 4.2 years ago by 3.6k • written 4.2 years ago by • 0
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4.1k
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monocle error at orderCells
scRNA monocle packages Tutorial
4.3 years ago 444579004 • 0
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EnsemblGene ID conversion
deseq2 annotation Tutorial
updated 4.3 years ago by 25k • written 4.3 years ago by • 0
0
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R Version 3.6.1
software error Tutorial
updated 4.3 years ago by 1.6k • written 4.3 years ago by • 0
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Tutorial: Differential Methylation Analysis using ChAMP
champ Tutorial
updated 4.4 years ago by ▴ 270 • written 4.4 years ago by • 0
1
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1.7k
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Error on zlib.h while installing esATAC on Ubutu
software error esATAC zlib.h Ubuntu Tutorial
updated 4.4 years ago by 25k • written 4.4 years ago by • 0
0
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ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 4.4 years ago by 13k • written 4.4 years ago by • 0
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How to change font size in ClusterProfiler
clusterProfiler font size Tutorial
updated 4.6 years ago by 48k • written 4.6 years ago by • 0
1
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Tutorial: How to download reference genomes using the RBioMart from ensembl?
BioMart downloading reference genome alignment Tutorial
4.6 years ago jcollidelcs • 0
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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 4.7 years ago by 41k • written 4.7 years ago by • 0
0
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Tutorial: Reading csv file in minfi
minfi infinium 450K Tutorial
4.8 years ago lalchungnungabt17 • 0
5
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Setting gene expression thresholds for trajectory analysis using Monocle
monocle differential gene expression detectgenes function Tutorial
4.8 years ago S.Webb6 ▴ 40
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How to extract SNPs from multiple alignment fasta file?
snp multiple sequence alignment fasta Tutorial
updated 5.1 years ago by 25k • written 5.1 years ago by • 0
1
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trouble importing data for DEseq2 workflow
deseq2 tximport tximportdata pasilla Tutorial
updated 5.1 years ago by 41k • written 5.1 years ago by • 0
2
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1
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1.0k
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GSVA tutorial brainTxDb oligodendrocytic_dn neuronal_dn are same genesets
GSVA tutorial
updated 5.2 years ago by ★ 3.0k • written 5.2 years ago by ▴ 10
1
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4
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2.2k
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EdgeR filtering, gene expression, cpm cutoff
edger Tutorial
updated 5.3 years ago by ▴ 400 • written 5.3 years ago by • 0
2
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Change legend names when using plotBCV
edger plot Tutorial
updated 5.3 years ago by 48k • written 5.3 years ago by • 0
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running GEO series matrix file normalization and DEGs in limma
limma normalization Tutorial
updated 5.4 years ago by 64k • written 5.4 years ago by • 0
1
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Tutorial: Update gene symbols in GeneSetCollection
gseabase msigdb genesetcollection Tutorial
5.4 years ago t.kuilman 170
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Tutorial: Importing multiple .h5 files using tximport
tximport Tutorial
updated 5.6 years ago by 13k • written 5.6 years ago by ▴ 10
0
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6
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2.3k
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Tutorial: use deseq2 in asthma
deseq2 Tutorial
5.6 years ago krwyaong.ju • 0
1
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2.0k
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Beta-matrix - Differential methylation analysis
ChAMP tutorial
5.6 years ago Dave Emir • 0
1
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3
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1.9k
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Gene ID Duplicates
deseq2 genetics Tutorial
updated 5.7 years ago by 64k • written 5.7 years ago by • 0
21
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10
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Tutorial: Bioconductor on Coursera
mooc Tutorial
updated 5.7 years ago by • 0 • written 8.2 years ago by 6.5k
3
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5
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Tutorial: Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile
R GEO geoquery geoquery error message Tutorial
5.9 years ago martinguerrerog89 ▴ 20
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How to install MethylKit?
methylkit Tutorial
updated 6.0 years ago by 25k • written 6.0 years ago by • 0
0
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2
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1.2k
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normalizationFactors DESeq2 package
deseq2 Tutorial
updated 6.1 years ago by 48k • written 6.1 years ago by • 0
4
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5
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1.6k
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SC3 gene clusters
SC3 single cell single-cell Tutorial
updated 6.1 years ago by 25k • written 6.1 years ago by ▴ 20
0
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3
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2.1k
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Pathview -- Error in korg[ridx, coln] : subscript out of bounds
pathview korg subscript out of bounds Tutorial
updated 6.2 years ago by ★ 1.6k • written 6.2 years ago by • 0
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Comment: limma::voom vs edgeR::voomLmFit - when to use? by Gordon Smyth 48k
Reitering James' answer, there is no reason not to use `voomLmFit` if you were planning to follow `voom` by `lmFit`. The reason why `voomLm…
Answer: EdgeR: Exact test and glmQLFTest produce very different results by James W. MacDonald 64k
You should just use the quasi-likelihood pipeline, which controls type I error better than the exact test or likelihood ratio test.
Answer: limma::voom vs edgeR::voomLmFit - when to use? by James W. MacDonald 64k
The workflow you reference was written in 2018, and hasn't been updated since 2020, except for version bumps (it's meant to parallel an F10…
Comment: 'Subtracting' counts on basis of Negative control media and water samples by Karthik • 0
I have entered the picture only in the analysis stage - the sequencing has all been performed and done. > Besides, likely the noise level…
Comment: NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R by James W. MacDonald 64k
It does look like CBP2 is an HGNC symbol, not a protein ID though. ``` > z <- select(ws, "CPB2", c("gene_names","xref_geneid","xref_ensemb…
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Answer: limma::voom vs edgeR::voomLmFit - when to use?
A: DSS understanding delta option and posterior probability
Comment: Ensembl down???
Answer: How should I run ssGSEA Hallmark Enrichment Analysis?
Answer: tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
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