Bioconductor Tutorial

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Training Bioconductor Event Community Tutorial

12 months ago Maria Doyle ▴ 70

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beginner Bioconductor tutorial examples

updated 2.2 years ago by Gordon Smyth 50k • written 2.2 years ago by Sara • 0

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1.1k

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tutorial DESeq2 pasilla

3.2 years ago Carina • 0

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2.2k

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mass spectrometry proteomics metabolomics Tutorial

written 3.5 years ago by Johannes Rainer ★ 2.0k

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3.1k

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limma deseq2 Tutorial

updated 3.6 years ago by Gordon Smyth 50k • written 3.6 years ago by yuemolinn • 0

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907

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tximport Cufflink Tutorial

updated 3.6 years ago by Kevin Blighe ★ 3.9k • written 3.6 years ago by LeiaMax2020 • 0

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726

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deseq2 Tutorial

updated 3.7 years ago by Kevin Blighe ★ 3.9k • written 3.7 years ago by taniachavarria79 • 0

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1.2k

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clusterProfiler r Tutorial

updated 3.7 years ago by Kevin Blighe ★ 3.9k • written 3.7 years ago by adR ▴ 30

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896

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STRT-Seq single-cell tutorial

updated 3.8 years ago by Aaron Lun ★ 28k • written 3.8 years ago by tiphaine.martin • 0

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644

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deseq2 Tutorial

updated 3.9 years ago by Michael Love 41k • written 3.9 years ago by Anna.bramucci • 0

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1.7k

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bioconductor libdrstats Tutorial

updated 4.0 years ago by Laurent Gatto 1.6k • written 4.0 years ago by Leonardo Collado Torres ★ 1.0k

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2.1k

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software error Tutorial

updated 4.0 years ago by Zuguang Gu ▴ 260 • written 4.0 years ago by AR3513 • 0

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2.1k

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salmon tximeta Tutorial

4.0 years ago Michael Love 41k

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1.7k

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DEXSeq log2foldchange Tutorial

updated 2.6 years ago by rohitsatyam102 ▴ 20 • written 4.1 years ago by tmvarsha ▴ 20

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1.9k

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deseq2 Tutorial

updated 4.1 years ago by Michael Love 41k • written 4.1 years ago by Nas 1989 • 0

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9.2k

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curl biomart getBM Tutorial

updated 4.1 years ago by James W. MacDonald 65k • written 4.1 years ago by Ni-Ar ▴ 10

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2.9k

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R 3.6.2 update problems with igraph and phangorn update Phyloseq igraph phangorn Tutorial

updated 4.3 years ago by Martin Morgan 25k • written 4.3 years ago by crgarcia • 0

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12k

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deseq2 combat Knownbatcheffect Tutorial

updated 3.2 years ago by Samuel Daniel • 0 • written 4.5 years ago by rajeshparmar4 ▴ 10

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862

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DMCHMM Tutorial

updated 4.6 years ago by shepherl 3.8k • written 4.6 years ago by shokoohi • 0

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4.6k

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scRNA monocle packages Tutorial

4.7 years ago 444579004 • 0

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1.2k

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deseq2 annotation Tutorial

updated 4.7 years ago by Martin Morgan 25k • written 4.7 years ago by trumbia • 0

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3.5k

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software error Tutorial

updated 4.7 years ago by Laurent Gatto 1.6k • written 4.7 years ago by naeemurself • 0

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1.5k

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Tutorial annotation

updated 2.6 years ago by Kevin Blighe ★ 3.9k • written 4.7 years ago by prodhan82 ▴ 20

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1.8k

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software error esATAC zlib.h Ubuntu Tutorial

updated 4.8 years ago by Martin Morgan 25k • written 4.8 years ago by vedbar • 0

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1.7k

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ATACseqQC ATAC ATACseq software error Tutorial

updated 4.8 years ago by Steve Lianoglou ★ 13k • written 4.8 years ago by mbasam • 0

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2.1k

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champ Tutorial

updated 4.8 years ago by Yuan Tian ▴ 280 • written 4.8 years ago by learning.iq84 • 0

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1.8k

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clusterProfiler font size Tutorial

updated 5.0 years ago by Gordon Smyth 50k • written 5.0 years ago by bony.dekumar ▴ 10

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BioMart downloading reference genome alignment Tutorial

5.0 years ago jcollidelcs • 0

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1.4k

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deseq2 limma edger Tutorial

updated 5.1 years ago by Michael Love 41k • written 5.1 years ago by wwu222 • 0

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1.8k

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minfi infinium 450K Tutorial

5.2 years ago lalchungnungabt17 • 0

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8.9k

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support.bioconductor.org editor markdown updates Tutorial

updated 29 days ago by Mj.A. • 0 • written 5.2 years ago by shepherl 3.8k

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1.4k

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monocle differential gene expression detectgenes function Tutorial

5.2 years ago S.Webb6 ▴ 40

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1.4k

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snp multiple sequence alignment fasta Tutorial

updated 5.5 years ago by Martin Morgan 25k • written 5.5 years ago by pltbiotech_tkarthi • 0

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1.2k

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deseq2 tximport tximportdata pasilla Tutorial

updated 5.5 years ago by Michael Love 41k • written 5.5 years ago by Stanley Yang • 0

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1.1k

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GSVA tutorial

updated 5.6 years ago by Robert Castelo ★ 3.3k • written 5.6 years ago by owen.whitley ▴ 10

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2.6k

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edger Tutorial

updated 5.7 years ago by Hotz, Hans-Rudolf ▴ 400 • written 5.7 years ago by ilovesuperheroes1993 • 0

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1.3k

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edger plot Tutorial

updated 5.7 years ago by Gordon Smyth 50k • written 5.7 years ago by Juan • 0

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1.5k

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limma normalization Tutorial

updated 5.8 years ago by James W. MacDonald 65k • written 5.8 years ago by devarajsaranya • 0

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1.9k

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gseabase msigdb genesetcollection Tutorial

written 5.8 years ago by t.kuilman ▴ 170

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3.2k

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tximport Tutorial

updated 6.0 years ago by Steve Lianoglou ★ 13k • written 6.0 years ago by nelson.s.garcia ▴ 10

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2.5k

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deseq2 Tutorial

6.0 years ago krwyaong.ju • 0

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2.3k

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ChAMP tutorial

6.0 years ago Dave Emir • 0

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2.1k

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deseq2 genetics Tutorial

updated 6.1 years ago by James W. MacDonald 65k • written 6.1 years ago by anokhi1997 • 0

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4.9k

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R GEO geoquery geoquery error message Tutorial

6.3 years ago martinguerrerog89 ▴ 20

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1.5k

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methylkit Tutorial

updated 6.4 years ago by Martin Morgan 25k • written 6.4 years ago by s1432985 • 0

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1.4k

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deseq2 Tutorial

updated 6.5 years ago by Gordon Smyth 50k • written 6.5 years ago by mariamari693693 • 0

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1.8k

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SC3 single cell single-cell Tutorial

updated 6.5 years ago by Martin Morgan 25k • written 6.5 years ago by ahmed.elewa ▴ 20

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2.3k

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pathview korg subscript out of bounds Tutorial

updated 6.6 years ago by Luo Weijun ★ 1.6k • written 6.6 years ago by aacevedo • 0

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2.2k

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subversion bioc-devel package development usedevel Tutorial

6.7 years ago Bohdan Khomtchouk ▴ 10

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3.8k

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public data TCGA GTEx Tutorial

6.7 years ago shepherl 3.8k

50 results • Page 1 of 1

Recent ...

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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k

> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …

Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10

With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.

Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k

You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.

Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k

Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…

Comment: get BM error by James W. MacDonald 65k

I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…

Votes

C: when to apply quantile normalization with voom in limma/voom framework with RNA-

A: How to know if I should use voomWithQualityWeights() or not?

A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom

Answer: Log-cpm values from limma

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