Showing : Tutorial • reset
21
votes
10
replies
8.6k
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Tutorial: Bioconductor on Coursera
mooc Tutorial
updated 6.1 years ago by • 0 • written 8.6 years ago by ★ 6.5k
17
votes
4
replies
8.9k
views
Tutorial: Updated Support Site Editor
support.bioconductor.org editor markdown updates Tutorial
updated 23 days ago by • 0 • written 5.2 years ago by 3.8k
11
votes
0
replies
5.8k
views
Tutorial: Introduction to Bioconductor for high-throughput sequence analysis
GenomicRanges Annotation RNAseq visualization Tutorial
8.8 years ago Martin Morgan 25k
8
votes
0
replies
3.6k
views
Tutorial: Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq chipseq visualization metagenomics proteomics Tutorial
8.8 years ago Martin Morgan 25k
8
votes
4
replies
4.4k
views
Tutorial: Epigenomics RoadMap Project files now accessible via AnnotationHub
AnnotationHub Epigenomics BigData RoadMap Project NIH Tutorial
updated 7.0 years ago by • 0 • written 8.9 years ago by ▴ 390
8
votes
18
replies
12k
views
Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 3.2 years ago by • 0 • written 4.5 years ago by ▴ 10
7
votes
5
replies
6.0k
views
Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
written 8.9 years ago by 21k
7
votes
0
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3.7k
views
Tutorial: New edX "Data analysis for Life Sciences" module: High performance computing for reproducible genomics
annotation genomicranges visualization docker shiny Tutorial
8.1 years ago Vincent J. Carey, Jr. 6.7k
7
votes
2
replies
6.1k
views
Tutorial: Course Material from BioC 2015: Where Software and Biology Connect
bioc2015 course-material Tutorial
updated 8.7 years ago by ★ 8.2k • written 8.7 years ago by ▴ 390
7
votes
4
replies
3.0k
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
6
votes
1
reply
3.1k
views
Tutorial: BoF "Writing papers in Rmarkdown, BiocStyle... (and books, posters)"
biocstyle Rmarkdown Tutorial
6.7 years ago Wolfgang Huber ★ 13k
6
votes
1
reply
3.9k
views
Tutorial: Orchestrating a small, parallel, RNA-seq pre-processing workflow using R
rnaseq biocparallel workflows sra Tutorial
8.8 years ago Sean Davis 21k
5
votes
3
replies
1.3k
views
Setting gene expression thresholds for trajectory analysis using Monocle
monocle differential gene expression detectgenes function Tutorial
5.2 years ago S.Webb6 ▴ 40
5
votes
4
replies
1.7k
views
Is there any tutorial to perform Mouse/Human Transcriptome microarrays 1.0 ?
mta10 tutorial affy
updated 8.5 years ago by 65k • written 8.5 years ago by ▴ 40
5
votes
1
reply
3.2k
views
Tutorial: Prototyping An Analysis Pipeline For Lexogen 3'-UTR RNA-seq In Bioconductor
shortread rsubread ensembldb Tutorial
8.0 years ago phil.chapman ▴ 150
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
4
votes
0
replies
3.4k
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
4
votes
0
replies
2.0k
views
Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
4.0 years ago Michael Love 41k
3
votes
3
replies
1.6k
views
Calculation of Log2 fold change in DEXSeq
DEXSeq log2foldchange Tutorial
updated 2.6 years ago by ▴ 20 • written 4.0 years ago by ▴ 20
3
votes
8
replies
3.0k
views
Tutorial: "developing" with HDF5Array
hdf5 DelayedArray summarizedexperiment Tutorial
7.2 years ago Vincent J. Carey, Jr. 6.7k
3
votes
1
reply
2.2k
views
Tutorial: Mass Spectrometry Data Analysis with the Spectra Package
mass spectrometry proteomics metabolomics Tutorial
written 3.5 years ago by ★ 2.0k
3
votes
0
replies
3.8k
views
Tutorial: dplyr and the GEOmetadb package for mining NCBI GEO metadata
geometadb dplyr Tutorial
8.9 years ago Sean Davis 21k
3
votes
5
replies
4.9k
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
2
votes
3
replies
1.8k
views
Limma voom mechanism
rnaseq limma limma-voom Tutorial
updated 7.1 years ago by ★ 28k • written 7.1 years ago by • 0
2
votes
3
replies
1.2k
views
Adapting old Workshop to recent changes of the Limma package
limma microarray tutorial
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 40
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
6.7 years ago shepherl 3.8k
2
votes
2
replies
1.3k
views
Change legend names when using plotBCV
edger plot Tutorial
updated 5.7 years ago by 50k • written 5.7 years ago by • 0
2
votes
1
reply
1.1k
views
GSVA tutorial brainTxDb oligodendrocytic_dn neuronal_dn are same genesets
GSVA tutorial
updated 5.6 years ago by ★ 3.2k • written 5.6 years ago by ▴ 10
2
votes
5
replies
1.5k
views
Differential Gene Expression
deseq2 bioinformatics rna-seq Tutorial
updated 7.5 years ago by 41k • written 7.5 years ago by ▴ 10
1
vote
2
replies
2.3k
views
Beta-matrix - Differential methylation analysis
ChAMP tutorial
6.0 years ago Dave Emir • 0
1
vote
1
reply
1.5k
views
edgeR, DE between 4 different samples
edger differential gene expression GLM Tutorial
updated 8.0 years ago by 65k • written 8.0 years ago by • 0
1
vote
1
reply
1.9k
views
Tutorial: Update gene symbols in GeneSetCollection
gseabase msigdb genesetcollection Tutorial
written 5.8 years ago by ▴ 170
1
vote
4
replies
2.6k
views
EdgeR filtering, gene expression, cpm cutoff
edger Tutorial
updated 5.7 years ago by ▴ 400 • written 5.7 years ago by • 0
1
vote
2
replies
2.8k
views
Tutorial for RNA-Seq Data Analysis
rnaseq data analysis tutorial workflows differential gene expression
updated 7.0 years ago by ★ 28k • written 7.0 years ago by • 0
1
vote
1
reply
1.5k
views
Is there any R package for filtering out SNP markers?
Tutorial annotation
updated 2.6 years ago by ★ 3.9k • written 4.7 years ago by ▴ 20
1
vote
2
replies
1.9k
views
Tutorial: selecting result from deseq2
deseq2 Tutorial
updated 4.1 years ago by 41k • written 4.1 years ago by • 0
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
1
vote
3
replies
1.8k
views
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
1
vote
2
replies
1.2k
views
trouble importing data for DEseq2 workflow
deseq2 tximport tximportdata pasilla Tutorial
updated 5.5 years ago by 41k • written 5.5 years ago by • 0
1
vote
2
replies
886
views
question for "Chapter 24 Zeisel mouse brain (STRT-Seq) in single-cell"
STRT-Seq single-cell tutorial
updated 3.8 years ago by ★ 28k • written 3.8 years ago by • 0
1
vote
2
replies
1.6k
views
Cannot read plink files correctly
snprelate Tutorial
updated 6.9 years ago by ▴ 30 • written 6.9 years ago by • 0
1
vote
0
replies
3.1k
views
Tutorial: BoF Bioc2017: Infrastructure for efficient storage and processing of large-scale single-cell genomics data
single-cell objectstorage Tutorial
6.7 years ago shepherl 3.8k
1
vote
3
replies
1.1k
views
Unable to reproduce Pasilla dataset which fresh instalation
tutorial DESeq2 pasilla
3.2 years ago Carina • 0
1
vote
1
reply
1.0k
views
Bioinformatics exercises for beginner
beginner Bioconductor tutorial examples
updated 2.2 years ago by 50k • written 2.2 years ago by • 0
1
vote
8
replies
9.1k
views
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
1
vote
1
reply
2.0k
views
Tutorial: How to download reference genomes using the RBioMart from ensembl?
BioMart downloading reference genome alignment Tutorial
5.0 years ago jcollidelcs • 0
1
vote
1
reply
1.6k
views
Find Intron Length from Annotation File?
annotation arabidopsis thaliana Tutorial
updated 8.1 years ago by 25k • written 8.1 years ago by • 0
1
vote
3
replies
2.1k
views
Gene ID Duplicates
deseq2 genetics Tutorial
updated 6.0 years ago by 65k • written 6.0 years ago by • 0
0
votes
1
reply
638
views
DESeq2 Experiment Setup
deseq2 Tutorial
updated 3.9 years ago by 41k • written 3.9 years ago by • 0
0
votes
0
replies
1.5k
views
News: Announcing short course in computational proteomics, May 2-6, 2016, Boston MA
proteomics tutorial mass spectrometry computational biology News
8.2 years ago Olga Vitek ▴ 40
50 results • Page 1 of 1
Recent ...
Replies
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Usually I run `voomLmFit`, although in order to create the mean-variance trend plots for this particular post, I ran `voom`; I've checked -…
Comment: Error in champ.load(): The following specified files do not exist by Sherin • 0
it worked! thank you so much!!
Comment: Multi factor design edgeR/Deseq2 by Elizabeth • 0
Sorry I realise this thread is ancient, but I'm wondering why it's ok to remove the last column from the design matrix? Also, why this desi…
Comment: DESeq2 setting significant p-value by Michael Love 41k
It does not resort. Also the dataset and results will have the same row names from object creation throughout the analysis.
Comment: Input Question for deseq.r by ATpoint ★ 4.0k
It is unclear what "deseq.r" is. It is not part of DESeq2, and almost certainly no part of RSeqAn. Please add details, and keep in mind tha…
Votes
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
Comment: Reading huge bismark coverage files using bbseq::read.bismark
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