Showing : Tutorial • reset
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Bioinformatics exercises for beginner
beginner Bioconductor tutorial examples
updated 11 months ago by 47k • written 11 months ago by • 0
1
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1
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1.0k
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Is there any R package for filtering out SNP markers?
Tutorial annotation
updated 16 months ago by 3.7k • written 3.5 years ago by ▴ 20
7
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5
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4.7k
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Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
written 7.7 years ago by 21k
1
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3
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591
views
Unable to reproduce Pasilla dataset which fresh instalation
tutorial DESeq2 pasilla
24 months ago Carina • 0
3
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0
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1.2k
views
Tutorial: Mass Spectrometry Data Analysis with the Spectra Package
mass spectrometry proteomics metabolomics Tutorial
2.3 years ago Johannes Rainer ★ 2.0k
7
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4
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2.2k
views
Comparing DEseq2 and Limma program, results not consistent
limma deseq2 Tutorial
updated 2.4 years ago by 47k • written 2.4 years ago by • 0
0
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1
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535
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Can I apply tximport to transcript-level estimates obtained using cufflinks (cuffquant and cuffnorm) ??
tximport Cufflink Tutorial
updated 2.4 years ago by 3.7k • written 2.4 years ago by • 0
0
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1
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350
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Differential expression analysis comparison using more that two variables
deseq2 Tutorial
updated 2.5 years ago by 3.7k • written 2.5 years ago by • 0
0
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2
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751
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Warning messages: gseaKEGG
clusterProfiler r Tutorial
updated 2.5 years ago by 3.7k • written 2.5 years ago by ▴ 20
1
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2
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469
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question for "Chapter 24 Zeisel mouse brain (STRT-Seq) in single-cell"
STRT-Seq single-cell tutorial
updated 2.6 years ago by ★ 28k • written 2.6 years ago by • 0
0
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1
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336
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DESeq2 Experiment Setup
deseq2 Tutorial
updated 2.7 years ago by 39k • written 2.7 years ago by • 0
0
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0
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1.1k
views
Tutorial: [LIBD rstats club] Bioconductor overview
bioconductor libdrstats Tutorial
updated 2.8 years ago by 1.6k • written 2.8 years ago by ★ 1.0k
1
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5
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1.2k
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ComplexHeatmap - R Session aborted after calling Heatmap()
software error Tutorial
updated 2.8 years ago by ▴ 240 • written 2.8 years ago by • 0
4
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0
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1.3k
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Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
2.8 years ago Michael Love 39k
3
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3
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979
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Calculation of Log2 fold change in DEXSeq
DEXSeq log2foldchange Tutorial
updated 17 months ago by ▴ 20 • written 2.8 years ago by ▴ 20
1
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2
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1.2k
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Tutorial: selecting result from deseq2
deseq2 Tutorial
updated 2.9 years ago by 39k • written 2.9 years ago by • 0
1
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8
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4.5k
views
BioMart: curl option when using getBM in loop
curl biomart getBM Tutorial
updated 2.9 years ago by 62k • written 2.9 years ago by ▴ 10
0
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2
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2.1k
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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 3.1 years ago by 25k • written 3.1 years ago by • 0
8
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18
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8.3k
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Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 23 months ago by • 0 • written 3.3 years ago by ▴ 10
0
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2
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473
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Display number of downloads on a website
DMCHMM Tutorial
updated 3.4 years ago by 3.4k • written 3.4 years ago by • 0
0
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1
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2.9k
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monocle error at orderCells
scRNA monocle packages Tutorial
3.4 years ago 444579004 • 0
0
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5
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698
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EnsemblGene ID conversion
deseq2 annotation Tutorial
updated 3.5 years ago by 25k • written 3.5 years ago by • 0
0
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2
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2.9k
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R Version 3.6.1
software error Tutorial
updated 3.5 years ago by 1.6k • written 3.5 years ago by • 0
0
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1
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1.3k
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Tutorial: Differential Methylation Analysis using ChAMP
champ Tutorial
updated 3.6 years ago by ▴ 250 • written 3.6 years ago by • 0
1
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3
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1.3k
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Error on zlib.h while installing esATAC on Ubutu
software error esATAC zlib.h Ubuntu Tutorial
updated 3.6 years ago by 25k • written 3.6 years ago by • 0
0
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7
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1.1k
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ATACseqQC shiftGAlignmentsList leads to (all(elementNROWS)>3) is not TRUE error
ATACseqQC ATAC ATACseq software error Tutorial
updated 3.6 years ago by 13k • written 3.6 years ago by • 0
0
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1
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1.1k
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How to change font size in ClusterProfiler
clusterProfiler font size Tutorial
updated 3.8 years ago by 47k • written 3.8 years ago by • 0
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1
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1.2k
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Tutorial: How to download reference genomes using the RBioMart from ensembl?
BioMart downloading reference genome alignment Tutorial
3.8 years ago jcollidelcs • 0
0
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4
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759
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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 3.9 years ago by 39k • written 3.9 years ago by • 0
16
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1
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6.1k
views
Tutorial: Updated Support Site Editor
support.bioconductor.org editor markdown updates Tutorial
updated 3.9 years ago by • 0 • written 4.0 years ago by 3.4k
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0
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1.2k
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Tutorial: Reading csv file in minfi
minfi infinium 450K Tutorial
4.0 years ago lalchungnungabt17 • 0
5
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3
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873
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Setting gene expression thresholds for trajectory analysis using Monocle
monocle differential gene expression detectgenes function Tutorial
4.0 years ago S.Webb6 ▴ 40
0
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0
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943
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How to extract SNPs from multiple alignment fasta file?
snp multiple sequence alignment fasta Tutorial
updated 4.3 years ago by 25k • written 4.3 years ago by • 0
1
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2
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752
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trouble importing data for DEseq2 workflow
deseq2 tximport tximportdata pasilla Tutorial
updated 4.3 years ago by 39k • written 4.3 years ago by • 0
2
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1
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787
views
GSVA tutorial brainTxDb oligodendrocytic_dn neuronal_dn are same genesets
GSVA tutorial
updated 4.4 years ago by ★ 3.0k • written 4.4 years ago by ▴ 10
1
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4
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1.5k
views
EdgeR filtering, gene expression, cpm cutoff
edger Tutorial
updated 4.5 years ago by ▴ 400 • written 4.5 years ago by • 0
2
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2
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820
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Change legend names when using plotBCV
edger plot Tutorial
updated 4.5 years ago by 47k • written 4.5 years ago by • 0
0
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3
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1.1k
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running GEO series matrix file normalization and DEGs in limma
limma normalization Tutorial
updated 4.6 years ago by 62k • written 4.6 years ago by • 0
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0
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1.3k
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Tutorial: Update gene symbols in GeneSetCollection
gseabase msigdb genesetcollection Tutorial
4.6 years ago t.kuilman 170
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4
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2.3k
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Tutorial: Importing multiple .h5 files using tximport
tximport Tutorial
updated 4.7 years ago by 13k • written 4.7 years ago by ▴ 10
0
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6
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1.7k
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Tutorial: use deseq2 in asthma
deseq2 Tutorial
4.8 years ago krwyaong.ju • 0
1
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2
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1.3k
views
Beta-matrix - Differential methylation analysis
ChAMP tutorial
4.8 years ago Dave Emir • 0
1
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3
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1.4k
views
Gene ID Duplicates
deseq2 genetics Tutorial
updated 4.8 years ago by 62k • written 4.8 years ago by • 0
21
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10
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7.3k
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Tutorial: Bioconductor on Coursera
mooc Tutorial
updated 4.9 years ago by • 0 • written 7.4 years ago by 6.5k
3
votes
5
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3.3k
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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
5.0 years ago martinguerrerog89 ▴ 20
0
votes
3
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982
views
How to install MethylKit?
methylkit Tutorial
updated 5.2 years ago by 25k • written 5.2 years ago by • 0
0
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2
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890
views
normalizationFactors DESeq2 package
deseq2 Tutorial
updated 5.3 years ago by 47k • written 5.3 years ago by • 0
4
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5
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1.1k
views
SC3 gene clusters
SC3 single cell single-cell Tutorial
updated 5.3 years ago by 25k • written 5.3 years ago by ▴ 20
0
votes
3
replies
1.6k
views
Pathview -- Error in korg[ridx, coln] : subscript out of bounds
pathview korg subscript out of bounds Tutorial
updated 5.4 years ago by ★ 1.6k • written 5.4 years ago by • 0
0
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0
replies
1.6k
views
Tutorial: Using Subversion to update /devel branch of Bioconductor package
subversion bioc-devel package development usedevel Tutorial
5.5 years ago Bohdan Khomtchouk ▴ 10
50 results • Page 1 of 1
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Answer: struggling to create a heatmap by ATpoint ★ 2.1k
I am reluctant to read through that wall of code. Here is what would work. Note that prefiltering makes sense before, not after running `DE…
Answer: collapseReplicates error after tximeta by Michael Love 39k
The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it by ATpoint ★ 2.1k
That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
Answer: Which genes are outliers in DESeq2? by ATpoint ★ 2.1k
You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…
Answer: Which genes are outliers in DESeq2? by Michael Love 39k
Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…
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Significant reporter activity with mpralm function
Answer: I cannot install annotables package in Rstudio (macOS)
Answer: log2 of normalized counts for further analyzes
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
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