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transcriptomics
•
reset
0
votes
4
replies
701
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor
Transcriptomics
DifferentialExpression
DESeq2
10 months ago
sreeshmaraj72
• 0
4
votes
6
replies
1.3k
views
How to best visualize multi-level transcriptomics experiment data?
ggplot2
Transcriptomics
Visualization
R
limma
22 months ago
mohammedtoufiq91
▴ 10
3
votes
4
replies
1.3k
views
Writing a loop to clean up protein names
Proteomics
Transcriptomics
Loops
batch-processing
R
updated 5.5 years ago by
Sebastian Gibb
▴ 80 • written 5.5 years ago by
laural710
• 0
4
votes
8
replies
1.2k
views
DESEQ2 - What is the recommended workflow in terms of pre-filtering and counts normalization?
DESeq2
Transcriptomics
updated 11 months ago by
Wolfgang Huber
★ 13k • written 11 months ago by
Peter
▴ 20
0
votes
4
replies
1.0k
views
GOexpress - Error when plotting expression data
RNA-seq
transcriptomics
gene ontology
gene expression
GOexpress
updated 4.2 years ago by
kevin.rue
▴ 350 • written 4.2 years ago by
atorson
• 0
1
vote
1
reply
868
views
NanoStringDiff Not Recognized as Numeric
Bioconductor
Transcriptomics
NanoStringDiff
updated 3.4 years ago by
Laurent Gatto
1.6k • written 3.4 years ago by
Pedro
▴ 10
5
votes
5
replies
2.4k
views
analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO
RNASeqR
Transcriptomics
updated 3.1 years ago by
James W. MacDonald
65k • written 3.1 years ago by
H. Z. Amini
▴ 10
0
votes
1
reply
729
views
Metatranscriptomics DESeq2 multifactorial sampling
Transcriptomics
DESeq2
updated 3.0 years ago by
Michael Love
41k • written 3.0 years ago by
seppe.demits
• 0
0
votes
3
replies
697
views
Understanding edgeR differential expression results
Transcriptomics
edgeR
DifferentialExpression
RNASeqData
RNASeq
updated 13 months ago by
Gordon Smyth
50k • written 13 months ago by
Teresa
• 0
1
vote
2
replies
1.2k
views
Not many DE genes using glmTreat
EdgeR
Bioinformatics
Transcriptomics
Quantseq
2.6 years ago
Barista
• 0
4
votes
5
replies
1.5k
views
EnhancedVolcano - Unable to customize the length of Connectors to Gene Labels
Transcriptomics
EnhancedVolcano
updated 11 months ago by
Kevin Blighe
★ 3.9k • written 11 months ago by
Peter
▴ 20
0
votes
1
reply
305
views
Time change in expression vs time change in phenotype
Transcriptomics
ExpressionData
DESeq2
updated 11 months ago by
Michael Love
41k • written 11 months ago by
Ivan
• 0
2
votes
2
replies
781
views
Deseq2 Resul variation by LFC variation
rnaseqGene
DESeq2
Transcriptomics
2.5 years ago • updated 10 months ago
diangomaiga
• 0
2
votes
5
replies
1.3k
views
DESeq2 with baseline correction for gene expression differences
DESeq2
edgeR
Transcriptomics
updated 2.1 years ago by
Michael Love
41k • written 2.1 years ago by
R1337
• 0
0
votes
1
reply
1.1k
views
Variance stabilization transformation (VST), blind=TRUE
DESeq2
Transcriptomics
RNASeq
updated 14 months ago by
Michael Love
41k • written 14 months ago by
Jayesh Kumar
• 0
0
votes
3
replies
904
views
DESeq2 - transcript length correction necessary when quantifying reads from ends of transcripts?
Transcriptomics
DESeq2
20 months ago
marius.wenzel
• 0
3
votes
2
replies
117
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
3 days ago
Anita
▴ 10
0
votes
2
replies
910
views
Downloading org.Mm.eg.db after R reinstall
org.Mmu.eg.db
Transcriptomics
3.0 years ago
Kate
• 0
0
votes
2
replies
656
views
Questions about `collapseReplicates` function in DESeq2
DESeq2
Transcriptomics
17 months ago
Yijing
• 0
2
votes
1
reply
1.4k
views
Understanding tximport working with salmon outputs
Transcriptomics
tximport
updated 18 months ago by
ATpoint
★ 4.0k • written 18 months ago by
Florent
▴ 10
3
votes
5
replies
1.2k
views
DESeq2, time-course interpretation
Transcriptomics
TimeCourse
DESeq2
updated 8 months ago by
Michael Love
41k • written 8 months ago by
smac97
• 0
1
vote
3
replies
1.0k
views
Identifying DEG between development stages
plant
Transcriptomics
DESeq2
r
updated 2.0 years ago by
Basti
▴ 750 • written 2.0 years ago by
cicely.day
• 0
0
votes
1
reply
663
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 14 months ago by
Dario Strbenac
★ 1.5k • written 14 months ago by
Hicham
▴ 10
1
vote
1
reply
887
views
cpm filtering parameter
cpm filtering
transcriptomics
rnaseq
edgeR
metatranscriptomics
updated 4.5 years ago by
Gordon Smyth
50k • written 4.5 years ago by
vm.higareda
▴ 10
2
votes
2
replies
2.7k
views
How adjusted p-values are calculated in limma
limma
r
transcriptomics
FDR
statistics
updated 4.5 years ago by
Gordon Smyth
50k • written 4.5 years ago by
Wuschel
▴ 10
0
votes
0
replies
753
views
How to integrate and visualize RNASeq / Proteomics data for metabolomics pathways?
r
metabolomics
KEGG
Proteomics
Transcriptomics
5.0 years ago
Wuschel
▴ 10
1
vote
1
reply
1.4k
views
News:
Bioinformatics Summer School - July 2019 - UCLouvain (Belgium)
RNAseq
deseq2
proteomics
transcriptomics
workshop
News
written 5.1 years ago by
Laurent Gatto
1.6k
2
votes
0
replies
2.3k
views
Job:
Bioconductor infrastructure for the integration of genomics, transcriptomics and proteomics data
proteomics
genomics
transcriptomics
software
Job
4.5 years ago
Laurent Gatto
1.6k
1
vote
0
replies
1.6k
views
Job:
Full time and permanent research logistician in Bioinformatics
transcriptomics
proteomics
job
bioinformatician
Job
5.1 years ago • updated 5.0 years ago
Laurent Gatto
1.6k
1
vote
0
replies
830
views
Job:
Bioinformatics PhD: The circadian clock in the ageing plant, University of York, UK
transcriptomics
gene expression
time series
plant biology
circadian
Job
4.5 years ago
dezer
▴ 10
0
votes
0
replies
739
views
Job:
Bionformatician in personalized oncotherapy (BEL)
job
bioinformatician
immunotherapy
genomics
transcriptomics
Job
4.3 years ago
cedric
• 0
0
votes
0
replies
834
views
Job:
Bioinformatics Scientist, CNS Transcriptomics at Alnylam Pharmaceuticals, Cambridge MA, USA
scRNA-seq
CNS
transcriptomics
RNAi
Job
4.2 years ago
Joseph Barry
▴ 10
0
votes
0
replies
858
views
Job:
Senior Bioinformatician - University of Alabama at Birmingham
JobPosting
Transcriptomics
SingleCell
RNA-seq
2.7 years ago
lianov
• 0
1
vote
0
replies
927
views
News:
News: Bioinformatics Summer School - July 2020 - UCLouvain (Belgium)
rnaseq
course
proteomics
transcriptomics
scrnaseq
News
4.1 years ago
Laurent Gatto
1.6k
0
votes
0
replies
668
views
Problems with cummeRbund
plot
transcriptomics
differential expression
cummeRbund
4.0 years ago
raquelponti
• 0
0
votes
0
replies
773
views
Job:
[apply by 8/15] PhD scholarship on functional and evolutionary genomics
JobPosting
Transcriptomics
GenomicVariation
2.7 years ago
marie
• 0
0
votes
0
replies
881
views
Job:
Computational Biologist at Denali Therapeutics
Transcriptomics
SingleCell
JobPosting
3.2 years ago
Steve Lianoglou
★ 13k
0
votes
0
replies
562
views
Job:
EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq
Transcriptomics
Pathways
Epigenetics
RNASeq
16 months ago
whduke
• 0
0
votes
0
replies
913
views
Job:
Bioinformatician at MiroBio, Oxford, UK
Transcriptomics
Bioconductor
Statistics
Job
Biocon
3.1 years ago
m.jackson
• 0
0
votes
0
replies
492
views
WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network
Transcriptomics
MicrobiomeData
RNASEQ
WCGNA
18 months ago
Julieta
• 0
0
votes
0
replies
895
views
Consensus wgcna soft threshold for each data
Transcriptomics
WGCNA
wgcna
3.0 years ago
2323982403
▴ 60
0
votes
0
replies
491
views
EdgeR without replication
Transcriptomics
16 months ago
kuttibiotech2009
• 0
0
votes
0
replies
896
views
Job:
Bionformatician Position / Heidelberg
neuroscience
data integration
transcriptomics
Job
5.0 years ago • updated 4.9 years ago
slezak
• 0
0
votes
0
replies
511
views
Analysis of TIF-seq data to generate transcription start sites (TSS) and poly(A) site (PAS) clusters
Transcriptomics
SequencingData
16 months ago
Rom
• 0
44 results • Page
1 of 1
Recent ...
Replies
Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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