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Tutorial: Updated Support Site Editor
support.bioconductor.org editor markdown updates Tutorial
updated 11 months ago by • 0 • written 6.1 years ago by 4.1k
0
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News: Include your Bioconductor tutorial in Smörgåsbord 2023, May 22-26!
Training Bioconductor Event Community Tutorial
22 months ago Maria Doyle ▴ 100
1
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1
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1.5k
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Bioinformatics exercises for beginner
beginner Bioconductor tutorial examples
updated 3.1 years ago by 52k • written 3.1 years ago by • 0
1
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1
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1.9k
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Is there any R package for filtering out SNP markers?
Tutorial annotation
updated 3.4 years ago by ★ 4.0k • written 5.6 years ago by ▴ 20
7
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5
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6.8k
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Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
written 9.8 years ago by 21k
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3
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1.5k
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Unable to reproduce Pasilla dataset which fresh instalation
tutorial DESeq2 pasilla
4.1 years ago Carina • 0
3
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1
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3.0k
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Tutorial: Mass Spectrometry Data Analysis with the Spectra Package
mass spectrometry proteomics metabolomics Tutorial
written 4.4 years ago by ★ 2.1k
7
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4
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4.0k
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Comparing DEseq2 and Limma program, results not consistent
limma deseq2 Tutorial
updated 4.4 years ago by 52k • written 4.5 years ago by • 0
0
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1
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1.1k
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Can I apply tximport to transcript-level estimates obtained using cufflinks (cuffquant and cuffnorm) ??
tximport Cufflink Tutorial
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by • 0
0
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1
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937
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Differential expression analysis comparison using more that two variables
deseq2 Tutorial
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by • 0
0
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2
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1.6k
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Warning messages: gseaKEGG
clusterProfiler r Tutorial
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by ▴ 40
1
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2
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1.2k
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question for "Chapter 24 Zeisel mouse brain (STRT-Seq) in single-cell"
STRT-Seq single-cell tutorial
updated 4.7 years ago by ★ 28k • written 4.7 years ago by • 0
0
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1
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839
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DESeq2 Experiment Setup
deseq2 Tutorial
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
0
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0
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2.2k
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Tutorial: [LIBD rstats club] Bioconductor overview
bioconductor libdrstats Tutorial
updated 4.9 years ago by 1.6k • written 4.9 years ago by ★ 1.1k
1
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5
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2.7k
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ComplexHeatmap - R Session aborted after calling Heatmap()
software error Tutorial
updated 4.9 years ago by ▴ 290 • written 4.9 years ago by • 0
4
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0
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2.6k
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Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
4.9 years ago Michael Love 43k
3
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3
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2.2k
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Calculation of Log2 fold change in DEXSeq
DEXSeq log2foldchange Tutorial
updated 3.5 years ago by ▴ 20 • written 4.9 years ago by ▴ 20
1
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2
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2.5k
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Tutorial: selecting result from deseq2
deseq2 Tutorial
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
1
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8
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12k
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BioMart: curl option when using getBM in loop
curl biomart getBM Tutorial
updated 5.0 years ago by 68k • written 5.0 years ago by ▴ 10
0
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2
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3.4k
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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 5.2 years ago by 25k • written 5.2 years ago by • 0
8
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18
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15k
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Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 4.1 years ago by • 0 • written 5.4 years ago by ▴ 10
0
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2
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1.1k
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Display number of downloads on a website
DMCHMM Tutorial
updated 5.5 years ago by 4.1k • written 5.5 years ago by • 0
0
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1
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5.6k
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monocle error at orderCells
scRNA monocle packages Tutorial
5.5 years ago 444579004 • 0
0
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5
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1.5k
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EnsemblGene ID conversion
deseq2 annotation Tutorial
updated 5.6 years ago by 25k • written 5.6 years ago by • 0
0
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2
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3.9k
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R Version 3.6.1
software error Tutorial
updated 5.6 years ago by 1.6k • written 5.6 years ago by • 0
0
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1
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2.7k
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Tutorial: Differential Methylation Analysis using ChAMP
champ Tutorial
updated 5.7 years ago by ▴ 290 • written 5.7 years ago by • 0
1
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3
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2.2k
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Error on zlib.h while installing esATAC on Ubutu
software error esATAC zlib.h Ubuntu Tutorial
updated 5.7 years ago by 25k • written 5.7 years ago by • 0
0
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7
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2.2k
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ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 5.7 years ago by ★ 13k • written 5.7 years ago by • 0
0
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1
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2.5k
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How to change font size in ClusterProfiler
clusterProfiler font size Tutorial
updated 5.9 years ago by 52k • written 5.9 years ago by ▴ 10
1
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1
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2.6k
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Tutorial: How to download reference genomes using the RBioMart from ensembl?
BioMart downloading reference genome alignment Tutorial
5.9 years ago jcollidelcs • 0
0
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4
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2.0k
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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 6.0 years ago by 43k • written 6.0 years ago by • 0
0
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0
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2.3k
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Tutorial: Reading csv file in minfi
minfi infinium 450K Tutorial
6.0 years ago lalchungnungabt17 • 0
5
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3
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1.8k
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Setting gene expression thresholds for trajectory analysis using Monocle
monocle differential gene expression detectgenes function Tutorial
6.1 years ago S.Webb6 ▴ 40
0
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0
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1.7k
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How to extract SNPs from multiple alignment fasta file?
snp multiple sequence alignment fasta Tutorial
updated 6.4 years ago by 25k • written 6.4 years ago by • 0
1
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2
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1.4k
views
trouble importing data for DEseq2 workflow
deseq2 tximport tximportdata pasilla Tutorial
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
2
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1
reply
1.4k
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GSVA tutorial brainTxDb oligodendrocytic_dn neuronal_dn are same genesets
GSVA tutorial
updated 6.5 years ago by ★ 3.4k • written 6.5 years ago by ▴ 10
1
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4
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3.4k
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EdgeR filtering, gene expression, cpm cutoff
edger Tutorial
updated 6.5 years ago by ▴ 400 • written 6.5 years ago by • 0
2
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2
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1.6k
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Change legend names when using plotBCV
edger plot Tutorial
updated 6.6 years ago by 52k • written 6.6 years ago by • 0
0
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3
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1.8k
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running GEO series matrix file normalization and DEGs in limma
limma normalization Tutorial
updated 6.7 years ago by 68k • written 6.7 years ago by • 0
1
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1
reply
2.3k
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Tutorial: Update gene symbols in GeneSetCollection
gseabase msigdb genesetcollection Tutorial
written 6.7 years ago by ▴ 170
0
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4
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3.9k
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Tutorial: Importing multiple .h5 files using tximport
tximport Tutorial
updated 6.8 years ago by ★ 13k • written 6.8 years ago by ▴ 10
0
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6
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3.1k
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Tutorial: use deseq2 in asthma
deseq2 Tutorial
6.9 years ago krwyaong.ju • 0
1
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2
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3.0k
views
Beta-matrix - Differential methylation analysis
ChAMP tutorial
6.9 years ago Dave Emir • 0
1
vote
3
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2.4k
views
Gene ID Duplicates
deseq2 genetics Tutorial
updated 6.9 years ago by 68k • written 6.9 years ago by • 0
21
votes
10
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9.5k
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Tutorial: Bioconductor on Coursera
mooc Tutorial
updated 7.0 years ago by • 0 • written 9.5 years ago by ★ 6.5k
3
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5
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5.9k
views
Tutorial: Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile
R GEO geoquery geoquery error message Tutorial
7.1 years ago martinguerrerog89 ▴ 20
0
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3
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2.1k
views
How to install MethylKit?
methylkit Tutorial
updated 7.3 years ago by 25k • written 7.3 years ago by • 0
0
votes
2
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1.7k
views
normalizationFactors DESeq2 package
deseq2 Tutorial
updated 7.4 years ago by 52k • written 7.4 years ago by • 0
4
votes
5
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2.2k
views
SC3 gene clusters
SC3 single cell single-cell Tutorial
updated 7.4 years ago by 25k • written 7.4 years ago by ▴ 20
0
votes
3
replies
2.8k
views
Pathview -- Error in korg[ridx, coln] : subscript out of bounds
pathview korg subscript out of bounds Tutorial
updated 7.5 years ago by ★ 1.6k • written 7.5 years ago by • 0
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Answer: Using tximport for kallisto aligned TOIL data by James W. MacDonald 68k
If you just have the transcript data, you probably don't need (and maybe cannot use) `tximport`. Instead you could just do the naive thing …
Answer: Reading gene expression data in GPR format and converting it to xlsx format by James W. MacDonald 68k
Setting aside the inadvisability of putting these data into Excel (and I should point out that these data are not single-cell, but instead …
Comment: concentration tables suitable as input for new packages? by wilkinson • 0
I am grateful for your response. Software such as "Spectra" may parse MS-data to generate tables of concentrations, for instance. But inste…
Comment: Removing UTR from GTF for gene quantification by ATpoint ★ 4.7k
Consider asking at biostars or bioinformatics reddit, since this is not directly related to a Bioconductor problem. Anyway, a couple of th…
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Hoover • 0
I got it! ([Drift Boss][1]) [1]: https://driftbossgame.co
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Answer: Differential expression of proteins using somascan data
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Handle zero effective gene length when tximport RSEM results
Handle zero effective gene length when tximport RSEM results
How to remove genes with 0 counts in tximport?
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