0
votes
1
reply
739
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 22 months ago by 53k • written 22 months ago by ▴ 180
2
votes
2
replies
1.0k
views
between lane normalization upper quantile
EDASeq edgeR
22 months ago elesofi • 0
2
votes
3
replies
3.7k
views
Fail BiocManager::install(version='3.12')
BioManager
updated 22 months ago by ★ 5.0k • written 3.8 years ago by ▴ 20
0
votes
1
reply
740
views
problem with ClusterRepro function
WGCNA
updated 22 months ago by 68k • written 22 months ago by • 0
0
votes
2
replies
1.3k
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 22 months ago by 43k • written 22 months ago by • 0
0
votes
4
replies
927
views
DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 22 months ago by 43k • written 22 months ago by • 0
2
votes
2
replies
912
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
22 months ago Sabiha ▴ 20
0
votes
10
replies
1.9k
views
DESeq2 filtering vs edgeR filtering
DESeq2
written 22 months ago by • 0
0
votes
2
replies
994
views
Scores used for DiffBind's dba.plotHeatmap
DiffBind
22 months ago Sam ▴ 10
0
votes
2
replies
3.7k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
22 months ago kcarey • 0
1
vote
1
reply
618
views
i'm not getting any differentially expressed genes.
DESeq2
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
2
votes
1
reply
862
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
0
votes
1
reply
834
views
Exact same results in Diffbind with different normalization methods
DiffBind
22 months ago red_bricks ▴ 60
0
votes
0
replies
633
views
FELLA plotGraph function won't change the legend
FELLA
22 months ago yuhang • 0
0
votes
0
replies
518
views
medips-output
ngsReports MEDIPS
22 months ago Researcher ▴ 10
1
vote
1
reply
806
views
Join BOC Sciences at Drug Discovery Chemistry
alabaster.schemas db0
updated 3 months ago by • 0 • written 22 months ago by ▴ 10
0
votes
1
reply
639
views
Syntenet error in infer_syntenet() Error in blast_list[[1]] : subscript out of bounds
syntenet
updated 22 months ago by ▴ 40 • written 24 months ago by • 0
0
votes
1
reply
726
views
question about data processing for syntenet
syntenet
updated 22 months ago by ▴ 40 • written 2.1 years ago by • 0
0
votes
4
replies
826
views
Error in classify_gene_pairs
syntenet doubletrouble
22 months ago hfyuan2016 • 0
2
votes
1
reply
789
views
Is random access by row index possible for an indexed VCF file?
Rsamtools VariantAnnotation
updated 22 months ago by 68k • written 22 months ago by ▴ 180
0
votes
0
replies
441
views
The graphical interface of FELLA doesn't work
FELLA
22 months ago yuhang • 0
0
votes
0
replies
532
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
22 months ago jean-christophe.helbling • 0
1
vote
1
reply
553
views
Perform PCA for sample clustering using DESeq2
DESeq2
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
1
vote
3
replies
1.1k
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 24 months ago by • 0
0
votes
2
replies
1.0k
views
DESeq2: Comparing A Knockout to a Strain
DESeq2
22 months ago Viktor Thiel • 0
0
votes
0
replies
739
views
To analyze StringTie data using the isoformSwitchAnalyzeR package
IsoformSwitchAnalyzeR
22 months ago Henry • 0
0
votes
1
reply
1.3k
views
Rcpp compilation error
Release Rcpp
updated 22 months ago by ★ 5.0k • written 22 months ago by ▴ 40
0
votes
1
reply
849
views
Rain error: invalid annotation of time points
rain
updated 12 months ago by • 0 • written 22 months ago by • 0
0
votes
0
replies
813
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi minfiDataEPIC
23 months ago Felix • 0
0
votes
1
reply
963
views
DESeq2 for pseudobulk analysis of scCITE-seq
DESeq2 scCITE-seq
updated 22 months ago by ★ 5.0k • written 23 months ago by • 0
1
vote
2
replies
816
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq Bioconductor rtracklayer
23 months ago thomas • 0
1
vote
1
reply
666
views
Error with BSgenome, wanting to analyse non-model species with ATACseqQC
ATACseqQC
updated 23 months ago by 68k • written 23 months ago by • 0
0
votes
8
replies
1.7k
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
23 months ago michelafrancesconi8 • 0
0
votes
1
reply
716
views
Unusually large fold-changes in Deseq2 results
DESeq2
updated 23 months ago by ★ 5.0k • written 23 months ago by • 0
0
votes
1
reply
753
views
News: Join BOC Sciences at Drug Discovery Chemistry 2024
DFP
written 23 months ago by • 0
2
votes
6
replies
1.7k
views
limma: vooma mean-variance trend and data filtration
MicroarrayData limma
23 months ago • updated 22 months ago Lily Cheang ▴ 10
3
votes
8
replies
1.5k
views
Constrast for Time Course Experiments using Limma
limma
23 months ago dl17032000 • 0
1
vote
4
replies
981
views
DESeq2 Replicates
DESeq2 RNASeq
23 months ago kcarey • 0
2
votes
6
replies
1.2k
views
Factor vs Character in design
DESeq2
23 months ago James Aiden • 0
1
vote
3
replies
1.1k
views
Dispersion estimation step is very slow with latest DESeq2 and glmGamPoi
DESeq2 glmGamPoi
23 months ago I-Hsuan Lin ▴ 10
4
votes
7
replies
2.0k
views
weird volcano plot
DESeq2
updated 23 months ago by • 0 • written 2.2 years ago by ▴ 10
0
votes
1
reply
796
views
DEseq2 dispersion plot
DESeq2
updated 23 months ago by 43k • written 23 months ago by • 0
1
vote
0
replies
721
views
News: Nominations for Bioconductor Awards 2024!
Recognition Awards Bioconductor Bioc2024
23 months ago shepherl 4.3k
0
votes
2
replies
1.1k
views
News: BioC2024 abstract submission is open!
BioC2024 Conference Bioconductor
written 23 months ago by ▴ 110
0
votes
0
replies
643
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
23 months ago • updated 22 months ago Giovanni Calice ▴ 160
0
votes
0
replies
1.1k
views
Job: Bioinformatics Spatial Omics and Proteomics Postdoc (Research Officer / Senior Research Officer) at WEHI (Melbourne, Australia)
Proteomics JobPosting SingleCell Spatial SpatialExperiment
23 months ago Peter Hickey ▴ 760
1
vote
3
replies
2.3k
views
Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
23 months ago • updated 16 months ago s.malik • 0
0
votes
0
replies
1.1k
views
Error: grouping factors must have > 1 sampled level
Mast mastR MAST
updated 23 months ago by 68k • written 23 months ago by • 0
0
votes
0
replies
730
views
News: Online course: Mass Spectrometry and Proteomics with R/Bioconductor
MSnbase
23 months ago info ▴ 10
1
vote
1
reply
1.2k
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 23 months ago by ★ 3.6k • written 23 months ago by • 0
46,730 results • Page 30 of 935
Recent ...
Replies
Comment: Bile acid analysis with limpa by ATpoint ★ 5.0k
Wilcox/Mann-Whitney-U cannot work because it is bound to sample size even when all of group X are lower than all of group Y. At 4 vs 3 the …
Comment: chemmineOB install help by Jeremy • 0
I could install ChemmineOB on my MacBook Pro M1 Max using this procedure **1. Install open-babel and eigen using homebrew and create a cus…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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