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News:
Bioconductor Community Advisory Board Members
news
bioconductor oversight
community
News
5.8 years ago
Matthew Ritchie
▴ 1000
1
vote
2
replies
1.0k
views
How to set model formulae in DEXSeq when 2 shRNAs were used to target a same gene
DEXSeq
updated 5.8 years ago by
Alejandro Reyes
★ 1.9k • written 5.8 years ago by
zliu
▴ 10
0
votes
1
reply
1.5k
views
Removing low sequences before analysis
deseq2
normalization
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
mpuli011
• 0
1
vote
1
reply
839
views
Differential Expression by Chromosome using edgeR
edgeR
chromosome
RNAseq
updated 5.8 years ago by
swbarnes2
★ 1.4k • written 5.8 years ago by
missmoparker
• 0
0
votes
9
replies
2.0k
views
Plotting change over time
deseq2
Plot
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
mpuli011
• 0
3
votes
5
replies
3.2k
views
How to analyze pre-processed RNA-Seq data from GEO based on the deseq R package for filtering and DE analysis
deseq
rna-seq
filtering
DE
deseq2
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
svlachavas
▴ 840
5
votes
8
replies
1.7k
views
Tibble error when installing bioconductor "airways"
airway
5.8 years ago
brest
• 0
1
vote
6
replies
4.5k
views
Which of these (raw count, scaled estimate, normalized_results ) data of TCGA is best for finding the DEG (differentially expressed) genes by DESeq2 …
deseq2
5.8 years ago
roohallah1435
• 0
0
votes
2
replies
1.5k
views
vmatchPattern error using a DNA string and BSgenome
Biostrings
vmatchPattern
BSgenome
5.8 years ago
mb2subi
• 0
0
votes
4
replies
1.7k
views
<N/A> Gene Ontology while using the AnnotationDbi package
go
annotation
annotationdbi
5.8 years ago
CUCIO199
• 0
0
votes
0
replies
838
views
Inter-chip methylation normalization
minfi
5.8 years ago
blawney
• 0
1
vote
5
replies
2.5k
views
AnnotationHub; Error: failed to load resource; Timeout was reached: [annotationhub.bioconductor.org]
annotationhub
updated 5.8 years ago by
shepherl
4.3k • written 5.8 years ago by
dilaik
• 0
4
votes
4
replies
4.4k
views
RNA seq analysis using Deseq2 and apeglm lfc shrinkage
deseq2
fdrtool
apeglm
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
Paul
• 0
1
vote
1
reply
1.6k
views
Problem downloading TCGA projects with the method "client"
bioconductor
GDCdownload
5.8 years ago
sann
• 0
0
votes
0
replies
427
views
Removing unused samples when estimating dispersion with EdgeR?
edger
5.8 years ago
elise.skottene
• 0
0
votes
1
reply
666
views
Should rows with zero sum be excluded before calling the DEseq() function
deseq2
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
megapode32559
• 0
0
votes
8
replies
2.4k
views
SingleR analysis with just a subset of Immgen data
annotation
updated 5.8 years ago by
Aaron Lun
★ 29k • written 5.8 years ago by
dangm
▴ 10
0
votes
2
replies
2.2k
views
Recount2 Bigwigs for TCGA
R
TCGA
recount2
recount
updated 5.8 years ago by
Leonardo Collado Torres
★ 1.1k • written 5.9 years ago by
alex.v.nesta
• 0
0
votes
1
reply
976
views
Affymetrix microarray - Limma on timepoint experiment, how to make the design and contrast matrix ?
limma
R
microarray
timepoint
affy
updated 5.8 years ago by
shepherl
4.3k • written 5.8 years ago by
ashwinmenon1994
• 0
0
votes
0
replies
1.1k
views
Problems with cummeRbund
plot
transcriptomics
differential expression
cummeRbund
5.8 years ago
raquelponti
• 0
0
votes
0
replies
753
views
ChAMP DMP col abbreviations stend for what?
ChAMP
5.8 years ago
julie
• 0
0
votes
1
reply
1.9k
views
Job:
Bioconductor is hiring!!
bioconductor
full-time
Job
5.8 years ago
shepherl
4.3k
0
votes
5
replies
2.8k
views
rtracklayer::import() BigWig issue on windows (solved)
software error
BigWig
import
windows
5.8 years ago
lsilva.m
• 0
0
votes
1
reply
759
views
Length scaled TPM and orthologous genes, from Tximport package
normalization
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
cossardg
▴ 10
0
votes
3
replies
1.6k
views
Nested design- phyloseq_to_deseq
deseq2
Phyloseq
Nested
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
mpuli011
• 0
0
votes
3
replies
691
views
Big difference between two-factor comparison when 3 factors data or when 2 factor data are used?
deseq2
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
megapode32559
• 0
0
votes
1
reply
1.4k
views
R circlize package problem with drawing histogram
circlize
R
Circos
Plots
5.8 years ago
marvel479
• 0
0
votes
2
replies
3.0k
views
Error in martCheck(mart, c("ensembl", "ENSEMBL_MART_ENSEMBL")) : No dataset selected, please select a dataset first.
biomart
mart
ensembl
updated 5.8 years ago by
James W. MacDonald
68k • written 5.8 years ago by
didemdkn
• 0
2
votes
3
replies
2.5k
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb
hg19
ucsc
seqlevel
genomicfeatures
updated 5.8 years ago by
James W. MacDonald
68k • written 5.8 years ago by
foehn
▴ 100
0
votes
2
replies
1.3k
views
DESEQ2: Error in checkFullRank(modelMatrix)
deseq2
miRNASeq
designmatrix
Batch
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
anshulmbi
• 0
0
votes
1
reply
1.6k
views
News:
New Package and New Docker Image Submission Deadline for Bioc Release 3.11
release
package submission
docker
deadline
News
5.9 years ago • updated 5.8 years ago
shepherl
4.3k
0
votes
0
replies
1.1k
views
News:
Deadline for devel branch 3.11 to pass R CMD build and R CMD check
release
devel
bioconductor
News
5.8 years ago
shepherl
4.3k
4
votes
6
replies
1.3k
views
mean log2CPM after model fit (lmFit)
limma
lmFit
mean expression level
updated 5.8 years ago by
James W. MacDonald
68k • written 5.8 years ago by
anna
• 0
0
votes
0
replies
1.1k
views
News:
Bioconductor Release 3.10 Code Freeze Deadline
release
deadline
bioconductor
News
5.8 years ago
shepherl
4.3k
0
votes
2
replies
1.2k
views
Does biovizBase contain a genesymbol data set for other model organisms?
biovizBase
ggbio
updated 5.8 years ago by
James W. MacDonald
68k • written 5.8 years ago by
moldach
▴ 20
0
votes
1
reply
619
views
DESeq2 - groups with no replicates
deseq2
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
august
• 0
2
votes
1
reply
1.5k
views
Maximum parsimony protein assembly/inference
rforproteomics
proteomics
msnid
msnbase
5.8 years ago
daniel.magnus.bader
▴ 50
0
votes
1
reply
1.1k
views
maEndtoEnd does not load on Mac version 3.6.0 or 3.6.2
maEndtoEnd
5.8 years ago
Ndimensional
▴ 20
1
vote
7
replies
1.1k
views
EdgeR design matrix question
edger
updated 5.8 years ago by
Gordon Smyth
53k • written 5.8 years ago by
jcrowdis
• 0
1
vote
2
replies
2.9k
views
selecting result from deseq2
DESeq2
updated 4 months ago by
Michael Love
43k • written 5.8 years ago by
Nas 1989
• 0
0
votes
1
reply
855
views
What happens when estimateSizeFactors() is added to the standard workflow before DESeq()?
deseq2
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
megapode32559
• 0
0
votes
1
reply
1.3k
views
My problem in MAGeCKFlute
software error
5.8 years ago
1092787384
• 0
0
votes
1
reply
1.1k
views
using deseq2 for intronic counts for 2 conditins with replicates
deseq2
intron
differential expression
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
gv
▴ 30
1
vote
8
replies
3.4k
views
Rsubread - Error on buildindex - big ref sequence
Rsubread
5.9 years ago • updated 13 months ago
bryan.penning
• 0
1
vote
2
replies
2.2k
views
how to integrate multiple samples from ADT-seq (CITE-seq) with fastMNN
fastMNN
CITE-seq
ADT-seq
batchelor
REAP-seq
updated 5.8 years ago by
Aaron Lun
★ 29k • written 5.8 years ago by
sorjuelal
• 0
0
votes
0
replies
858
views
MeDIP seq data analysis
medip_seq
Macs
5.8 years ago
Mar Mar
▴ 20
1
vote
2
replies
4.8k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
featureCounts
5.8 years ago
chatterjee.arumoy
▴ 10
2
votes
1
reply
1.3k
views
Should I use factors for covariate in limma design matrix or not?
limma
updated 5.8 years ago by
James W. MacDonald
68k • written 5.8 years ago by
msveldhuis96
• 0
0
votes
1
reply
5.5k
views
How to modify label text size/line width in cnetplot (ReactomePA/clusterProfiler)
clusterProfiler
ReactomePA
updated 5.8 years ago by
Guangchuang Yu
★ 1.2k • written 5.8 years ago by
liampvmartin1992
▴ 10
0
votes
0
replies
1.1k
views
News:
Bioconductor 3.11 db0s are available
annotation
db0
news
release
News
5.8 years ago
kayla.interdonato
▴ 160
46,730 results • Page
173 of 935
Recent ...
Replies
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…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
I don't think DESeq2 has the ability to do multi-contrast comparisons, at least based on what I can understand of the manual; I can pick mu…
Comment: Upcoming Ensembl API and data access changes - new blog post available
by
Hugo Gruson
• 0
Thanks for the update. To be very explicit: what is going to happen to the Biomart service, on which the biomaRt bioconductor package relie…
Comment: Are individual-mouse-based statistics possible in CellChat?
by
LillianaVolkman99
• 0
thank you very much. https://www.biostars.org/p/9617271/
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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