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Showing :
Transcriptomics
•
reset
3
votes
2
replies
124
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
4 days ago • updated 3 days ago
Anita
▴ 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
0
votes
4
replies
703
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor
Transcriptomics
DifferentialExpression
DESeq2
10 months ago
sreeshmaraj72
• 0
0
votes
1
reply
306
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
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
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
3
replies
699
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
0
votes
1
reply
665
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
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
0
replies
493
views
EdgeR without replication
Transcriptomics
16 months ago
kuttibiotech2009
• 0
0
votes
0
replies
514
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
0
votes
0
replies
563
views
Job:
EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq
Transcriptomics
Pathways
Epigenetics
RNASeq
16 months ago
whduke
• 0
0
votes
2
replies
658
views
Questions about `collapseReplicates` function in DESeq2
DESeq2
Transcriptomics
17 months ago
Yijing
• 0
0
votes
0
replies
493
views
WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network
Transcriptomics
MicrobiomeData
RNASEQ
WCGNA
18 months ago
Julieta
• 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
0
votes
3
replies
906
views
DESeq2 - transcript length correction necessary when quantifying reads from ends of transcripts?
Transcriptomics
DESeq2
20 months ago
marius.wenzel
• 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
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
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
2
votes
2
replies
782
views
Deseq2 Resul variation by LFC variation
rnaseqGene
DESeq2
Transcriptomics
2.5 years ago • updated 10 months ago
diangomaiga
• 0
1
vote
2
replies
1.2k
views
Not many DE genes using glmTreat
EdgeR
Bioinformatics
Transcriptomics
Quantseq
2.6 years ago
Barista
• 0
0
votes
0
replies
860
views
Job:
Senior Bioinformatician - University of Alabama at Birmingham
JobPosting
Transcriptomics
SingleCell
RNA-seq
2.7 years ago
lianov
• 0
0
votes
0
replies
775
views
Job:
[apply by 8/15] PhD scholarship on functional and evolutionary genomics
JobPosting
Transcriptomics
GenomicVariation
2.7 years ago
marie
• 0
0
votes
2
replies
911
views
Downloading org.Mm.eg.db after R reinstall
org.Mmu.eg.db
Transcriptomics
3.0 years ago
Kate
• 0
0
votes
0
replies
898
views
Consensus wgcna soft threshold for each data
Transcriptomics
WGCNA
wgcna
3.0 years ago
2323982403
▴ 60
0
votes
1
reply
730
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
0
replies
914
views
Job:
Bioinformatician at MiroBio, Oxford, UK
Transcriptomics
Bioconductor
Statistics
Job
Biocon
3.1 years ago
m.jackson
• 0
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
0
replies
884
views
Job:
Computational Biologist at Denali Therapeutics
Transcriptomics
SingleCell
JobPosting
3.2 years ago
Steve Lianoglou
★ 13k
1
vote
1
reply
869
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
0
votes
0
replies
670
views
Problems with cummeRbund
plot
transcriptomics
differential expression
cummeRbund
4.0 years ago
raquelponti
• 0
1
vote
0
replies
928
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
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
0
votes
0
replies
835
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
740
views
Job:
Bionformatician in personalized oncotherapy (BEL)
job
bioinformatician
immunotherapy
genomics
transcriptomics
Job
4.3 years ago
cedric
• 0
1
vote
0
replies
834
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
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
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
1
reply
890
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
0
votes
0
replies
754
views
How to integrate and visualize RNASeq / Proteomics data for metabolomics pathways?
r
metabolomics
KEGG
Proteomics
Transcriptomics
5.0 years ago
Wuschel
▴ 10
0
votes
0
replies
899
views
Job:
Bionformatician Position / Heidelberg
neuroscience
data integration
transcriptomics
Job
5.0 years ago • updated 4.9 years ago
slezak
• 0
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
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
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
44 results • Page
1 of 1
Recent ...
Replies
Comment: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Comment: fgsea fork
by
shepherl
3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Answer: Doing comparison of RNA-seq data using EdgeR
by
Gordon Smyth
50k
It's pretty easy to do a two-group comparison using edgeR, but you seem to be stuck at the initial stage of reading data into R. If you exp…
Answer: Differing results from plotMDS and PCAtools
by
Gordon Smyth
50k
The reason why the two plots are different is that the first plot is a PCA plot while the second is a biplot. Quite different plots. The P…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
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
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