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Tutorial: Updated Support Site Editor
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updated 11 days ago by • 0 • written 6.6 years ago by 4.2k
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News: Include your Bioconductor tutorial in Smörgåsbord 2023, May 22-26!
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2.3 years ago Maria Doyle ▴ 100
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Bioinformatics exercises for beginner
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updated 3.5 years ago by 52k • written 3.5 years ago by • 0
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Is there any R package for filtering out SNP markers?
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updated 3.9 years ago by ★ 4.0k • written 6.1 years ago by ▴ 20
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Tutorial: Accessing Public Genomic Data from Bioconductor
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4.6 years ago Carina • 0
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Tutorial: Mass Spectrometry Data Analysis with the Spectra Package
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written 4.9 years ago by ★ 2.1k
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updated 4.9 years ago by 52k • written 4.9 years ago by • 0
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1.2k
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Can I apply tximport to transcript-level estimates obtained using cufflinks (cuffquant and cuffnorm) ??
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updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by • 0
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Differential expression analysis comparison using more that two variables
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updated 5.0 years ago by ★ 4.0k • written 5.0 years ago by • 0
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updated 5.0 years ago by ★ 4.0k • written 5.1 years ago by ▴ 40
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updated 5.2 years ago by ★ 29k • written 5.2 years ago by • 0
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931
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DESeq2 Experiment Setup
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updated 5.3 years ago by 43k • written 5.3 years ago by • 0
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updated 5.3 years ago by 1.6k • written 5.3 years ago by ★ 1.1k
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ComplexHeatmap - R Session aborted after calling Heatmap()
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updated 5.3 years ago by ▴ 290 • written 5.3 years ago by • 0
4
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5.4 years ago Michael Love 43k
3
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updated 4.0 years ago by ▴ 20 • written 5.4 years ago by ▴ 20
1
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Tutorial: selecting result from deseq2
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updated 5.4 years ago by 43k • written 5.4 years ago by • 0
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8
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updated 5.4 years ago by 68k • written 5.5 years ago by ▴ 10
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updated 5.7 years ago by 25k • written 5.7 years ago by • 0
8
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18
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Batch correction by using ComBat function in sva package
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updated 4.5 years ago by • 0 • written 5.9 years ago by ▴ 10
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6.0 years ago 444579004 • 0
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updated 6.0 years ago by 25k • written 6.0 years ago by • 0
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Tutorial: Differential Methylation Analysis using ChAMP
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updated 6.2 years ago by ▴ 290 • written 6.2 years ago by • 0
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updated 6.2 years ago by 25k • written 6.2 years ago by • 0
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updated 6.2 years ago by ★ 13k • written 6.2 years ago by • 0
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updated 6.3 years ago by 52k • written 6.3 years ago by ▴ 10
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Tutorial: How to download reference genomes using the RBioMart from ensembl?
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6.4 years ago jcollidelcs • 0
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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?
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updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
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6.5 years ago lalchungnungabt17 • 0
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6.6 years ago S.Webb6 ▴ 40
0
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1.8k
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How to extract SNPs from multiple alignment fasta file?
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updated 6.9 years ago by 25k • written 6.9 years ago by • 0
1
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updated 6.9 years ago by 43k • written 6.9 years ago by • 0
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GSVA tutorial brainTxDb oligodendrocytic_dn neuronal_dn are same genesets
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updated 7.0 years ago by ★ 3.4k • written 7.0 years ago by ▴ 10
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updated 7.0 years ago by ▴ 400 • written 7.0 years ago by • 0
2
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updated 7.1 years ago by 52k • written 7.1 years ago by • 0
0
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3
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running GEO series matrix file normalization and DEGs in limma
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updated 7.1 years ago by 68k • written 7.1 years ago by • 0
1
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2.5k
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Tutorial: Update gene symbols in GeneSetCollection
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written 7.2 years ago by ▴ 170
0
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4
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Tutorial: Importing multiple .h5 files using tximport
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updated 7.3 years ago by ★ 13k • written 7.3 years ago by ▴ 10
0
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6
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3.4k
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Tutorial: use deseq2 in asthma
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7.4 years ago krwyaong.ju • 0
1
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2
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3.3k
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Beta-matrix - Differential methylation analysis
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7.4 years ago Dave Emir • 0
1
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3
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2.7k
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Gene ID Duplicates
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updated 7.4 years ago by 68k • written 7.4 years ago by • 0
21
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10
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10.0k
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Tutorial: Bioconductor on Coursera
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updated 7.4 years ago by • 0 • written 10.0 years ago by ★ 6.5k
3
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5
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Tutorial: Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile
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7.6 years ago martinguerrerog89 ▴ 20
0
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How to install MethylKit?
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updated 7.8 years ago by 25k • written 7.8 years ago by • 0
0
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normalizationFactors DESeq2 package
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updated 7.8 years ago by 52k • written 7.8 years ago by • 0
4
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SC3 gene clusters
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updated 7.9 years ago by 25k • written 7.9 years ago by ▴ 20
0
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3
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Pathview -- Error in korg[ridx, coln] : subscript out of bounds
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updated 7.9 years ago by ★ 1.6k • written 8.0 years ago by • 0
80 results • Page 1 of 2
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Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by James W. MacDonald 68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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