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0
votes
3
replies
1.2k
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diffbind analyze for wheat
DiffBind
updated 21 months ago by
Igor
• 0 • written 2.3 years ago by
zgyu12
• 0
0
votes
1
reply
860
views
How to compared two groups out of twelve in DESeq2
DESeq2
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
paige.ramkissoon
• 0
7
votes
6
replies
9.1k
views
Conversion of UniProt to Ensembl
biomaRt
ensembldb
UniProt.ws
updated 2.2 years ago by
Marcel Ramos
700 • written 3.3 years ago by
Recep
▴ 20
1
vote
5
replies
1.3k
views
Why do I obtain Identical Adj.P value when running edgeR ?
edgeR
updated 2.3 years ago by
Gordon Smyth
53k • written 2.3 years ago by
Mohamed
▴ 30
1
vote
7
replies
1.9k
views
Permutation test in DESeq2?
DESeq2
updated 2.3 years ago by
Michael Love
43k • written 2.3 years ago by
michellewei
• 0
0
votes
6
replies
1.5k
views
Help with model.matrix and creating the right contrast matrix for limma
limma
2.3 years ago • updated 2.0 years ago
rober204
• 0
0
votes
0
replies
636
views
CpG coverage with MEDIPS
MEDIPS
CpG
2.3 years ago
greta
• 0
0
votes
1
reply
739
views
Missing genes in the differentially expressed gene list which otherwise are expected to show expression post treatment.
MoleculeExperiment
updated 2.3 years ago by
ATpoint
★ 5.0k • written 2.3 years ago by
irenekokosaikia
• 0
3
votes
3
replies
1.1k
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest
edgeR
DESeq2
2.3 years ago
Nisha
• 0
0
votes
11
replies
3.5k
views
Support of parquet files for on-disk Bioconductor objects
DelayedArray
TileDBArray
updated 4 months ago by
Tasse
• 0 • written 2.3 years ago by
sandmann.t
▴ 70
3
votes
1
reply
927
views
NPARC package y-variable
NPARC
NPA
updated 2.3 years ago by
nils.kurzawa
▴ 20 • written 2.3 years ago by
Aidan
• 0
3
votes
5
replies
2.2k
views
Getting batch corrected counts after RUVSeq
BatchEffect
RUVSeq
RNASeq
DESeq2
updated 2.3 years ago by
ATpoint
★ 5.0k • written 2.3 years ago by
Shashank
• 0
1
vote
6
replies
3.4k
views
annotation EpicV2
minfiDataEPIC
EpicV2
updated 2.2 years ago by
Zuguang Gu
▴ 290 • written 2.3 years ago by
Izabela.ams
▴ 10
0
votes
1
reply
603
views
Run DESeq2 on chromosome and plasmids separately
DESeq2
updated 2.3 years ago by
ATpoint
★ 5.0k • written 2.3 years ago by
Laura
▴ 10
6
votes
5
replies
13k
views
Using Limma R package For Proteomics differential expression
limma
ProteomicsWorkflow
updated 2.3 years ago by
Gordon Smyth
53k • written 4.1 years ago by
David Lyon
▴ 340
0
votes
0
replies
704
views
Error ambiguity characters in sequences
BSgenomeForge
2.3 years ago
Bruno
• 0
4
votes
5
replies
1.6k
views
Phenotype effect - building a contrast matrix - grouping vs interaction
limma
updated 2.2 years ago by
Gordon Smyth
53k • written 2.3 years ago by
Jonathan
▴ 10
0
votes
3
replies
1.7k
views
BSgenome.Athaliana.TAIR.TAIR10.1
arabidopsis.db0
Arabidopsis_thaliana
Arabidopsis_thaliana_Data
2.3 years ago
Bruno
• 0
0
votes
1
reply
697
views
Unable to create ddf object
DESeqDataSetFromMatrix
dds
DESeq2
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
naomi.croft
• 0
0
votes
2
replies
989
views
Biomart - upstream region of 'coding'
biomaRt
updated 2.3 years ago by
Mike Smith
★ 6.6k • written 2.3 years ago by
andrebolerbarros
▴ 20
0
votes
2
replies
1.3k
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
2.3 years ago
Gerhard Thallinger
▴ 180
0
votes
2
replies
1.1k
views
RSubread DESeq2
RNASeqData
DifferentialExpression
DESeq2
2.3 years ago
Beyza
• 0
0
votes
1
reply
1.5k
views
mzR has been built against a different Rcpp version (1.0.10) than is installed on your system (1.0.11).
erah
mzR
Rcpp
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
tingting
• 0
1
vote
2
replies
2.2k
views
Cluster profiler emap plot - what are the annotations?
clusterProfiler
emapplot
2.3 years ago
fluentin44
• 0
1
vote
3
replies
1.3k
views
GOfuncR fails to build on Mac OS
GOfuncR
updated 22 months ago by
Steffi Grote
▴ 10 • written 2.3 years ago by
Marek Gierlinski
▴ 30
2
votes
3
replies
1.6k
views
Import Salmon data with tximport and pool technical replicates
tximport
edgeR
written 2.3 years ago by
Vitor
• 0
7
votes
2
replies
2.0k
views
Format roxgen comment (alternative to formatR)
BiocCheck
written 4.2 years ago by
ZheFrench
▴ 60
1
vote
1
reply
933
views
bulk RNA-Seq batch correction
RNASeqData
rnaseqcomp
RNASeq
updated 2.3 years ago by
ATpoint
★ 5.0k • written 2.3 years ago by
jg0428
• 0
0
votes
3
replies
963
views
Dramatically different DESeq2 results in Mac and Linux computers
DESeq2
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
jovel_juan
▴ 30
1
vote
2
replies
751
views
Setting up a multi-factor experiement
DESeq2
2.3 years ago • updated 2.2 years ago
jon50250
• 0
0
votes
1
reply
862
views
DESeq design and contrast with multiple factors
RNASeq
DESeq2
updated 2.3 years ago by
Michael Love
43k • written 2.3 years ago by
Adam
• 0
0
votes
0
replies
662
views
How to use erccdashboard with erccmix="Single" design
RNASeqData
erccdashboard
2.3 years ago
adi.rotem
• 0
1
vote
5
replies
1.3k
views
edgeR design/contrast matrix troubles
edgeR
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
alex.hart
• 0
0
votes
1
reply
627
views
`R CMD check` failure on Linux for diffcoexp
diffcoexp
written 2.4 years ago by
martin.grigorov
▴ 10
6
votes
5
replies
2.3k
views
error message when I use the bsseq read.bismark command to read a genome wide cytosine report generated by bismark.
bsseq
updated 2.3 years ago by
Peter Hickey
▴ 760 • written 2.4 years ago by
richardallenfriedmanbrooklyn
▴ 30
0
votes
1
reply
674
views
Barplot multicategory problems
vulcan
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
mavamay
• 0
0
votes
2
replies
4.0k
views
Error: BiocParallel errors
xcms
msdata
BiocParallel
2.3 years ago
mavamay
• 0
3
votes
13
replies
2.4k
views
Timely differentially expressed genes
timecoursedata
limma
2.3 years ago • updated 2.1 years ago
triZZla
• 0
0
votes
0
replies
550
views
maSigPro drug concentration
maSigPro
2.3 years ago
jiawen
• 0
1
vote
3
replies
1.3k
views
AAbin vs DNAbin structures
Biostrings
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
rogerb
• 0
0
votes
0
replies
1.6k
views
News:
Bioconductor 3.18 Release Schedule
Release
Software
release
2.3 years ago
shepherl
4.2k
0
votes
1
reply
965
views
GSVA exceeds 1
GSVA
updated 2.3 years ago by
Robert Castelo
★ 3.4k • written 2.3 years ago by
Heba
• 0
0
votes
0
replies
717
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 2.3 years ago by
Gordon Smyth
53k • written 2.3 years ago by
Cosmin Saveanu
• 0
0
votes
0
replies
726
views
HeatPlot - Genes selections
enrichplot
stringr
heatplot
2.3 years ago
ruba-mahmoud
• 0
0
votes
2
replies
2.3k
views
MACS2 not installing
Bioconductor
2.3 years ago
alia.sinqua
• 0
1
vote
1
reply
1.2k
views
results after deseq2 not showing gene ids and gene names but they are present in dds object
DESeq2
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
Anup
• 0
0
votes
3
replies
1.5k
views
DESeq2 not full rank with paired patient samples and one control cohort
DESeq2
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
The_T_cell_Guy
• 0
1
vote
0
replies
1.1k
views
News:
News: BioCAsia2023 Abstract Submission & Registration Now Open!
Events
BioCAsia
Conference
2.3 years ago
Maria Doyle
▴ 110
0
votes
2
replies
2.1k
views
Error: insufficient numeric precision during Log fold change shrinkage with apeglm
apeglm
updated 2.3 years ago by
Michael Love
43k • written 2.3 years ago by
Juan Pablo
• 0
0
votes
3
replies
1.4k
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq
RNA-seq
DESeq2
updated 2.3 years ago by
Alejandro Reyes
★ 1.9k • written 2.3 years ago by
Alice
• 0
46,695 results • Page
43 of 934
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Answer: NUPOP usage
by
shepherl
4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker?
by
fnfgame
• 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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