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Votes
2
votes
1
reply
2.4k
views
Software Compatibility Issue Between phyloseq and lme4 Packages
phyloseq
microbiome
Software
updated 2.3 years ago by
ATpoint
★ 5.0k • written 2.3 years ago by
HULFRED
▴ 10
0
votes
3
replies
997
views
The meaning of the analysis results when using a new metric in analysis
DESeq2
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
SH
▴ 10
1
vote
2
replies
928
views
RRID (unique searchable Research Resource Identifier ) of LymphoSeq
Clonality
2.3 years ago
Zijun
• 0
0
votes
0
replies
688
views
DTU analysis with factorial model
IsoformSwitchAnalyzeR
satuRn
2.3 years ago
jbono
▴ 10
1
vote
1
reply
1.6k
views
Can I transform already normalized rna-seq data with Z-score?
Z-score
RNASeqData
Deseq
DESeq2
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
khaserdene99
• 0
2
votes
3
replies
5.0k
views
TPM from STAR mapped counts
GeneExpression
GenomicFeatures
RNA-Seq
TPM
updated 2.3 years ago by
Gordon Smyth
53k • written 2.3 years ago by
gingergeiger22
• 0
3
votes
7
replies
1.8k
views
Genes in open chromatin region
ChIPpeakAnno
DiffBind
written 2.3 years ago by
Chris
▴ 20
0
votes
3
replies
1.2k
views
diffbind analyze for wheat
DiffBind
updated 22 months ago by
Igor
• 0 • written 2.3 years ago by
zgyu12
• 0
0
votes
1
reply
862
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
9.2k
views
Conversion of UniProt to Ensembl
biomaRt
ensembldb
UniProt.ws
updated 2.2 years ago by
Marcel Ramos
700 • written 3.4 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
1.6k
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
643
views
CpG coverage with MEDIPS
MEDIPS
CpG
2.3 years ago
greta
• 0
0
votes
1
reply
743
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
940
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
2.3k
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 2.3 years ago by
Zuguang Gu
▴ 290 • written 2.4 years ago by
Izabela.ams
▴ 10
0
votes
1
reply
607
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 4.2 years ago by
David Lyon
▴ 340
0
votes
0
replies
715
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 2.3 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
708
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
1.0k
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
2.3k
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 23 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 2.4 years ago by
Vitor
• 0
7
votes
2
replies
2.0k
views
Format roxgen comment (alternative to formatR)
BiocCheck
written 4.3 years ago by
ZheFrench
▴ 60
1
vote
1
reply
938
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
975
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
758
views
Setting up a multi-factor experiement
DESeq2
2.3 years ago • updated 2.2 years ago
jon50250
• 0
0
votes
1
reply
868
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
672
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
629
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
679
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
556
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
972
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
725
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
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