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More Web Proxy on the site http://driver.im/
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Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
bioconductor Install
8 months ago BioinfGuru ▴ 70
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1.5k
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Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
16 months ago Gordon Smyth 52k
17
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4
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9.9k
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Tutorial: Updated Support Site Editor
support.bioconductor.org editor markdown updates Tutorial
updated 9 months ago by • 0 • written 5.9 years ago by 4.1k
0
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2.0k
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Tutorial: Online workshop "Working with ChatGPT in R" 2023-03-09
chatgpt programming
updated 8 months ago by • 0 • written 22 months ago by ★ 13k
7
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5
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6.7k
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Tutorial: Accessing Public Genomic Data from Bioconductor
geoquery geometadb sradb Tutorial
written 9.6 years ago by 21k
3
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1
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2.8k
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Tutorial: Mass Spectrometry Data Analysis with the Spectra Package
mass spectrometry proteomics metabolomics Tutorial
written 4.2 years ago by ★ 2.1k
0
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0
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2.1k
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Tutorial: [LIBD rstats club] Bioconductor overview
bioconductor libdrstats Tutorial
updated 4.7 years ago by 1.6k • written 4.7 years ago by ★ 1.1k
4
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0
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2.5k
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Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
4.7 years ago Michael Love 43k
1
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2
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2.4k
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Tutorial: selecting result from deseq2
deseq2 Tutorial
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
0
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2.6k
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Tutorial: Differential Methylation Analysis using ChAMP
champ Tutorial
updated 5.5 years ago by ▴ 290 • written 5.5 years ago by • 0
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1
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2.5k
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Tutorial: How to download reference genomes using the RBioMart from ensembl?
BioMart downloading reference genome alignment Tutorial
5.7 years ago jcollidelcs • 0
0
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2.3k
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Tutorial: Reading csv file in minfi
minfi infinium 450K Tutorial
5.9 years ago lalchungnungabt17 • 0
1
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1
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2.2k
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Tutorial: Update gene symbols in GeneSetCollection
gseabase msigdb genesetcollection Tutorial
written 6.5 years ago by ▴ 170
0
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4
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3.8k
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Tutorial: Importing multiple .h5 files using tximport
tximport Tutorial
updated 6.7 years ago by ★ 13k • written 6.7 years ago by ▴ 10
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6
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3.0k
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Tutorial: use deseq2 in asthma
deseq2 Tutorial
6.7 years ago krwyaong.ju • 0
21
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10
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9.3k
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Tutorial: Bioconductor on Coursera
mooc Tutorial
updated 6.8 years ago by • 0 • written 9.3 years ago by ★ 6.5k
3
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5
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5.7k
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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
6.9 years ago martinguerrerog89 ▴ 20
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2.5k
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Tutorial: Using Subversion to update /devel branch of Bioconductor package
subversion bioc-devel package development usedevel Tutorial
7.4 years ago Bohdan Khomtchouk ▴ 10
2
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0
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Tutorial: BoF Bioc2017: Analyzing publicly available cancer genomics data from GTEx and TCGA with Bioconductor
public data TCGA GTEx Tutorial
7.4 years ago shepherl 4.1k
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Tutorial: BoF Bioc2017: Infrastructure for efficient storage and processing of large-scale single-cell genomics data
single-cell objectstorage Tutorial
7.4 years ago shepherl 4.1k
6
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3.5k
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Tutorial: BoF "Writing papers in Rmarkdown, BiocStyle... (and books, posters)"
biocstyle Rmarkdown Tutorial
7.4 years ago Wolfgang Huber ★ 13k
0
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2
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2.7k
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Tutorial: LEA won't run lfmm sequentially and independently on individual environmental variables when d set to 0
LEA lfmm Tutorial
updated 7.6 years ago by • 0 • written 7.6 years ago by • 0
8
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4
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4.9k
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Tutorial: Epigenomics RoadMap Project files now accessible via AnnotationHub
AnnotationHub Epigenomics BigData RoadMap Project NIH Tutorial
updated 7.7 years ago by • 0 • written 9.6 years ago by ▴ 390
3
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8
replies
3.5k
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Tutorial: "developing" with HDF5Array
hdf5 DelayedArray summarizedexperiment Tutorial
7.9 years ago Vincent J. Carey, Jr. 6.7k
0
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8.1k
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Tutorial: doParallel foreach already exporting variable(s)
doParallel foreach export Tutorial
7.9 years ago solo7773 ▴ 10
4
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0
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3.8k
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Tutorial: Workflow for low-level analysis of single-cell RNA-seq data
scran scater single cell Tutorial
8.3 years ago Aaron Lun ★ 28k
5
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1
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3.5k
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Tutorial: Prototyping An Analysis Pipeline For Lexogen 3'-UTR RNA-seq In Bioconductor
shortread rsubread ensembldb Tutorial
8.7 years ago phil.chapman ▴ 150
7
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0
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4.0k
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Tutorial: New edX "Data analysis for Life Sciences" module: High performance computing for reproducible genomics
annotation genomicranges visualization docker shiny Tutorial
8.8 years ago Vincent J. Carey, Jr. 6.7k
7
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2
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7.5k
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Tutorial: Course Material from BioC 2015: Where Software and Biology Connect
bioc2015 course-material Tutorial
updated 9.4 years ago by ★ 8.2k • written 9.4 years ago by ▴ 390
11
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0
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6.1k
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Tutorial: Introduction to Bioconductor for high-throughput sequence analysis
GenomicRanges Annotation RNAseq visualization Tutorial
9.5 years ago Martin Morgan 25k
6
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1
reply
4.2k
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Tutorial: Orchestrating a small, parallel, RNA-seq pre-processing workflow using R
rnaseq biocparallel workflows sra Tutorial
9.5 years ago Sean Davis 21k
8
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0
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3.8k
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Tutorial: Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq chipseq visualization metagenomics proteomics Tutorial
9.5 years ago Martin Morgan 25k
3
votes
0
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Tutorial: dplyr and the GEOmetadb package for mining NCBI GEO metadata
geometadb dplyr Tutorial
9.6 years ago Sean Davis 21k
33 results • Page 1 of 1
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Comment: Identifying potentially associated gene set to drug response using GSVA by coolmathforkids2 • 0
It is always helpful to see clear explanations and solutions for bioconductor related challenges. Posts like this make the community a valu…
Comment: minfi latest update for EPIC V2 chip by macdonaldfrench7286566 • 0
Yes, the most updated analysis for the EPIC V2 chip using the minfi package still involves using the annotations provided by jokergoo. *Th…
Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k
To compute CPM values from edgeR: ``` y <- DGEList(counts = counts, samples = samples, genes = genes, group = samples$Disease_status) y <- …
Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Gordon Smyth 52k
Follow the vignette. It explains how to call edgeR's cpm function to use the offsets.
Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Andre • 0
But if i want to do another type of analysis like Wilcoxon/Mann-Whitney and want to incorporate salmon offset can i simply use the cpm func…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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