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20
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3.9k
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DESeq2 question: why I got discrepancy results for DEGs when using different ways setting up the models
DESeq2
DEGs
4.5 years ago • updated 4.4 years ago
Ming
▴ 380
2
votes
8
replies
1.9k
views
pdInfoBuilder created problematic package for Affymetrix chip tiling array
oligoClasses
oligo
pdInfoBuilder
4.5 years ago • updated 4.4 years ago
efoss
▴ 10
3
votes
2
replies
4.3k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m31) is not TRUE
GenomeInfoDb
updated 4.5 years ago by
Rob Syme
▴ 20 • written 4.5 years ago by
jason.ossart
▴ 10
1
vote
6
replies
3.4k
views
deseq2 for TCGA tumor/normal paired sample from multiple patients
deseq2
updated 4.5 years ago by
Michael Love
43k • written 10.2 years ago by
luren
• 0
2
votes
3
replies
1.7k
views
importing RSEM isoform to Gene Name with tximport
tximport
updated 4.5 years ago by
James W. MacDonald
68k • written 4.5 years ago by
luca.s
▴ 50
0
votes
9
replies
2.3k
views
AnnotationHub: failed to load resource name
DFP
4.5 years ago
hxwanghxw
• 0
0
votes
1
reply
1.2k
views
Annotations do not load in shiny app
spatialLIBD
updated 4.4 years ago by
Leonardo Collado Torres
★ 1.1k • written 4.5 years ago by
Dimitri
• 0
1
vote
2
replies
1.2k
views
DiffBind dba.report(): Question about DBA_ALL_METHODS
DiffBind
4.5 years ago
etiennedanis
• 0
0
votes
1
reply
1.3k
views
can't install destiny package
destiny
updated 4.5 years ago by
Basti
▴ 780 • written 4.5 years ago by
chet.seligman
• 0
1
vote
5
replies
4.0k
views
undefined columns selected
DESeq2
updated 4.5 years ago by
Kevin Blighe
★ 4.0k • written 4.5 years ago by
waltsonwang88
• 0
1
vote
1
reply
5.9k
views
Processing Nanostring GeoMX Q3 normalized data as intensities with Limma
Limma
GeoMX
updated 4.4 years ago by
GeneEx
• 0 • written 4.5 years ago by
Matthew Thornton
▴ 390
0
votes
2
replies
2.2k
views
error in file(file, "rt") when reading in sample sheet using DESeqDataSetFromHTSeqCount
DESeq2
4.5 years ago
Yihan
• 0
1
vote
2
replies
1.0k
views
Doing multiple comparisons in a DESeq2 object with multiple conditions
DESeq2
4.5 years ago
jenabris
• 0
0
votes
0
replies
849
views
visualization of circRNA
circRNA
circRNAprofiler
4.5 years ago
Bogdan
▴ 670
2
votes
5
replies
2.5k
views
Downloading count matrix for full recount3 dataset
recount3
updated 22 months ago by
Leonardo Collado Torres
★ 1.1k • written 4.5 years ago by
Ben
• 0
1
vote
1
reply
1.3k
views
How to sort out error in gdcCEAnalysis function of GDCRNATools R package?
GDCRNATools
updated 4.5 years ago by
James W. MacDonald
68k • written 4.5 years ago by
Bhavya
• 0
3
votes
2
replies
1.5k
views
R NanoStringDiff: DE analysis, from 2 group comparison method how "logFC" generated?
Nan
NanoStringDiff
4.5 years ago
choijamts
• 0
0
votes
2
replies
2.0k
views
Error: $ operator is invalid for atomic vectors
import
4.5 years ago
Ofelia
• 0
1
vote
3
replies
1.2k
views
subset a list based on table
edgeR
RNASeq
resfilt
updated 4.5 years ago by
ATpoint
★ 5.0k • written 4.5 years ago by
najib
• 0
3
votes
16
replies
4.0k
views
DESeq2 - groups with biological replicates from the same patient
DESeq2
updated 24 months ago by
shepherl
4.3k • written 4.5 years ago by
S
▴ 10
0
votes
4
replies
2.9k
views
estimateSizeFactors throws "Error in .local(object, ..., value) : all(!is.na(value)) is not TRUE". Identified root cause within estimateSizeFactorsFo…
DESeq2
4.5 years ago
alawrence2211
• 0
3
votes
4
replies
4.8k
views
Clarification re VST transformed data in DESeq2
DESeq2
updated 4.5 years ago by
ATpoint
★ 5.0k • written 4.5 years ago by
Nikolay Ivanov
• 0
2
votes
9
replies
3.4k
views
extract fold change of a list of gene from EdgeR?
EdgeR
RNAseq
Foldchange
updated 4.5 years ago by
swbarnes2
★ 1.4k • written 4.5 years ago by
najib
• 0
1
vote
1
reply
6.0k
views
Installing hdf5r without admin access
hdf5r
installation
updated 4.5 years ago by
Hervé Pagès
16k • written 4.5 years ago by
snp31
• 0
0
votes
0
replies
1.1k
views
ImpulseDE2 Model Fits
ImpulseDE2
4.5 years ago
rohitghosh
• 0
1
vote
5
replies
7.5k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread
featureCounts
updated 2.5 years ago by
Yang Liao
▴ 450 • written 4.5 years ago by
s.muroy
▴ 10
0
votes
0
replies
680
views
gpuMagic with NVIDIA GeForce?
gpuMagic
4.5 years ago
Andrew
• 0
1
vote
2
replies
3.1k
views
How to fix .bam file that was diagnosed as "MISSING_READ_GROUP" by Picard ValidateSamFile
Picard
ValidateSamFile
MISSING_READ_GROUP
4.5 years ago
Michal
▴ 10
0
votes
2
replies
4.1k
views
EnsDb.Mmusculus.v79 : Failed to switch to UCSC style
Ensdb.M
EnsDb.Mmusculus.v79
updated 4.5 years ago by
jason.ossart
▴ 10 • written 4.5 years ago by
mostafa.eltager
• 0
0
votes
0
replies
1.2k
views
News:
Bioconductor 2021 Scholarship and Caregiver Awards
Bioc2021
Conference
4.5 years ago
shepherl
4.3k
1
vote
1
reply
931
views
How are greylists derived in DiffBind
DiffBind
updated 4.5 years ago by
Rory Stark
★ 5.2k • written 4.5 years ago by
Alexandre
▴ 10
2
votes
2
replies
3.2k
views
Questions regard to GSVA and Limma
limma
GSVA
4.5 years ago
Chenxi
• 0
2
votes
2
replies
1.4k
views
Turn of GSVA filtering for method ssGSEA
GSVA
4.5 years ago
k.vitting.seerup
▴ 120
0
votes
1
reply
1.5k
views
DESseq2 question about VST and rlog
DESeq2
Normalization
updated 4.5 years ago by
ATpoint
★ 5.0k • written 4.5 years ago by
Golden-proteogenomics
• 0
4
votes
7
replies
2.3k
views
Spline-fitted data analysis in edgeR question
edgeR
4.5 years ago
erik.burchard
• 0
0
votes
2
replies
2.7k
views
bcftools command not found
samtools
bcftools
updated 4.5 years ago by
Kevin Blighe
★ 4.0k • written 4.5 years ago by
mike_flower
• 0
0
votes
4
replies
2.7k
views
Error of read in large vcf file using readVcf
SomaticSignatures
VariantAnnotation
updated 4.5 years ago by
James W. MacDonald
68k • written 4.5 years ago by
xiw588
• 0
0
votes
5
replies
4.6k
views
Grange object subsetting using seqnames
Seqnames
makeGRangesFromDataFrame
GRanges
Subsetting
GenomicRanges
4.5 years ago
rtrivedi1
▴ 10
1
vote
0
replies
2.5k
views
Normalization of metabolomics/lipidomics data for limma
Lipidomics
Metabolomics
limma
Normalization
4.5 years ago
pgugger
▴ 70
0
votes
0
replies
996
views
Difficulty exporting consensus sequence from bam file
Rsamtools
sequenceLayer
4.5 years ago
mike_flower
• 0
2
votes
1
reply
1.0k
views
estimateSizeFactors before or after removing non-coding genes and filtering for low counts
DESeq2
RNASeq
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
Tash.
• 0
3
votes
3
replies
1.9k
views
How is DESeq2 handling replicates?
DESeq2
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
XTR5
▴ 10
0
votes
1
reply
1.5k
views
Differentially expressed genes across three different conditions
MAST
SingleCell
diffGeneAnalysis
updated 4.5 years ago by
James W. MacDonald
68k • written 4.5 years ago by
sofia.puvogel
• 0
0
votes
2
replies
1.6k
views
Can't retrieve upstream flank (biomaRt)
biomaRt
4.5 years ago
Pete
• 0
0
votes
3
replies
1.8k
views
pathview: unable to use option "out.suffix"
pathview
updated 4.5 years ago by
Luo Weijun
★ 1.6k • written 4.6 years ago by
文祥
• 0
0
votes
1
reply
1.4k
views
Adding insect abundance data to SparCC Analysis
sparcc
Microbiome
microbiomeExplorer
MicrobiomeData
updated 4.5 years ago by
Kevin Blighe
★ 4.0k • written 4.5 years ago by
GlycineMax
• 0
0
votes
6
replies
1.5k
views
Bias of lowly expressed genes in DESeq2
DESeq2
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
Jason
• 0
0
votes
2
replies
2.6k
views
DESeq2 for longitudinal data
DESeq2
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
lovelymaoqin
• 0
0
votes
1
reply
1.3k
views
Tool for simulating bulk RNA-Seq from single cell data
scRNAseq
updated 4.5 years ago by
James W. MacDonald
68k • written 4.5 years ago by
mpatino2799
• 0
0
votes
3
replies
1.4k
views
How to write a script for identifying associate gene id
bash
r
bingo
4.5 years ago • updated 3.1 years ago
abhisek001
• 0
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Comment: Opportunity to host EuroBioC2026 Preconference workshops!
by
TikTsokaas33ocissalpc
• 0
Thank you for sharing the EuroBioC2026 workshop opportunity. I m interested in hosting a hands on session teaching reproducible data analys…
Comment: Ensembl plants at annotationHub?
by
jwp48
• 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
Answer: Combining two proteomics datasets with limpa
by
Gordon Smyth
53k
Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Comment: Guitar R package requires update due to dependency GenomicFeatures
by
ferran.llobet.cabau
▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub?
by
Guido Hooiveld
★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
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Answer: Where do the filename come from in the LOLA datasets?
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Comment: Guitar R package requires update due to dependency GenomicFeatures
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