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Transcriptomics
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0
votes
4
replies
166
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problem while retriving the genes by using p value and log2fc as conditions
Bioconductor
Transcriptomics
DifferentialExpression
DESeq2
4 days ago • updated 3 days ago
sreeshmaraj72
• 0
0
votes
1
reply
93
views
Time change in expression vs time change in phenotype
Transcriptomics
ExpressionData
DESeq2
updated 5 weeks ago by
Michael Love
40k • written 5 weeks ago by
Ivan
• 0
3
votes
5
replies
219
views
EnhancedVolcano - Unable to customize the length of Connectors to Gene Labels
Transcriptomics
EnhancedVolcano
updated 6 weeks ago by
Kevin Blighe
3.8k • written 6 weeks ago by
Peter
▴ 10
4
votes
8
replies
377
views
DESEQ2 - What is the recommended workflow in terms of pre-filtering and counts normalization?
DESeq2
Transcriptomics
updated 6 weeks ago by
Wolfgang Huber
13k • written 7 weeks ago by
Peter
▴ 10
0
votes
3
replies
258
views
Understanding edgeR differential expression results
Transcriptomics
edgeR
DifferentialExpression
RNASeqData
RNASeq
updated 3 months ago by
Gordon Smyth
47k • written 3 months ago by
Teresa
• 0
0
votes
1
reply
235
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 4 months ago by
Dario Strbenac
★ 1.5k • written 4 months ago by
Hicham
• 0
0
votes
1
reply
287
views
Variance stabilization transformation (VST), blind=TRUE
DESeq2
Transcriptomics
RNASeq
updated 4 months ago by
Michael Love
40k • written 4 months ago by
Jayesh Kumar
• 0
0
votes
0
replies
211
views
EdgeR without replication
Transcriptomics
5 months ago
kuttibiotech2009
• 0
0
votes
0
replies
232
views
Analysis of TIF-seq data to generate transcription start sites (TSS) and poly(A) site (PAS) clusters
Transcriptomics
SequencingData
6 months ago
Rom
• 0
0
votes
0
replies
216
views
Job:
EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq
Transcriptomics
Pathways
Epigenetics
RNASeq
6 months ago
whduke
• 0
0
votes
2
replies
292
views
Questions about `collapseReplicates` function in DESeq2
DESeq2
Transcriptomics
7 months ago
Yijing
• 0
0
votes
0
replies
201
views
WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network
Transcriptomics
MicrobiomeData
RNASEQ
WCGNA
8 months ago
Julieta
• 0
2
votes
1
reply
563
views
Understanding tximport working with salmon outputs
Transcriptomics
tximport
updated 8 months ago by
ATpoint
★ 2.8k • written 8 months ago by
Florent
▴ 10
0
votes
3
replies
535
views
DESeq2 - transcript length correction necessary when quantifying reads from ends of transcripts?
Transcriptomics
DESeq2
10 months ago
marius.wenzel
• 0
4
votes
6
replies
780
views
How to best visualize multi-level transcriptomics experiment data?
ggplot2
Transcriptomics
Visualization
R
limma
12 months ago
mohammedtoufiq91
▴ 10
1
vote
3
replies
563
views
Identifying DEG between development stages
plant
Transcriptomics
DESeq2
r
updated 14 months ago by
Basti
▴ 720 • written 14 months ago by
cicely.day
• 0
2
votes
5
replies
818
views
DESeq2 with baseline correction for gene expression differences
DESeq2
edgeR
Transcriptomics
updated 15 months ago by
Michael Love
40k • written 15 months ago by
R1337
• 0
2
votes
2
replies
457
views
Deseq2 Resul variation by LFC variation
rnaseqGene
DESeq2
Transcriptomics
19 months ago • updated 7 days ago
diangomaiga
• 0
1
vote
2
replies
786
views
Not many DE genes using glmTreat
EdgeR
Bioinformatics
Transcriptomics
Quantseq
21 months ago
Barista
• 0
0
votes
0
replies
489
views
Job:
Senior Bioinformatician - University of Alabama at Birmingham
JobPosting
Transcriptomics
SingleCell
RNA-seq
22 months ago
lianov
• 0
0
votes
0
replies
484
views
Job:
[apply by 8/15] PhD scholarship on functional and evolutionary genomics
JobPosting
Transcriptomics
GenomicVariation
22 months ago
marie
• 0
0
votes
2
replies
615
views
Downloading org.Mm.eg.db after R reinstall
org.Mmu.eg.db
Transcriptomics
2.1 years ago
Kate
• 0
0
votes
0
replies
566
views
Consensus wgcna soft threshold for each data
Transcriptomics
WGCNA
wgcna
2.2 years ago
2323982403
▴ 50
0
votes
1
reply
468
views
Metatranscriptomics DESeq2 multifactorial sampling
Transcriptomics
DESeq2
updated 2.2 years ago by
Michael Love
40k • written 2.2 years ago by
seppe.demits
• 0
0
votes
0
replies
634
views
Job:
Bioinformatician at MiroBio, Oxford, UK
Transcriptomics
Bioconductor
Statistics
Job
Biocon
2.2 years ago
m.jackson
• 0
5
votes
5
replies
1.7k
views
analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO
RNASeqR
Transcriptomics
updated 2.3 years ago by
James W. MacDonald
62k • written 2.3 years ago by
H. Z. Amini
• 0
0
votes
0
replies
623
views
Job:
Computational Biologist at Denali Therapeutics
Transcriptomics
SingleCell
JobPosting
2.4 years ago
Steve Lianoglou
13k
1
vote
1
reply
615
views
NanoStringDiff Not Recognized as Numeric
Bioconductor
Transcriptomics
NanoStringDiff
updated 2.6 years ago by
Laurent Gatto
1.6k • written 2.6 years ago by
Pedro
▴ 10
0
votes
0
replies
423
views
Problems with cummeRbund
plot
transcriptomics
differential expression
cummeRbund
3.2 years ago
raquelponti
• 0
1
vote
0
replies
683
views
News:
News: Bioinformatics Summer School - July 2020 - UCLouvain (Belgium)
rnaseq
course
proteomics
transcriptomics
scrnaseq
News
3.3 years ago
Laurent Gatto
1.6k
0
votes
4
replies
647
views
GOexpress - Error when plotting expression data
RNA-seq
transcriptomics
gene ontology
gene expression
GOexpress
updated 3.3 years ago by
kevin.rue
▴ 320 • written 3.3 years ago by
atorson
• 0
0
votes
0
replies
532
views
Job:
Bioinformatics Scientist, CNS Transcriptomics at Alnylam Pharmaceuticals, Cambridge MA, USA
scRNA-seq
CNS
transcriptomics
RNAi
Job
3.4 years ago
Joseph Barry
▴ 10
0
votes
0
replies
520
views
Job:
Bionformatician in personalized oncotherapy (BEL)
job
bioinformatician
immunotherapy
genomics
transcriptomics
Job
3.5 years ago
cedric
• 0
1
vote
0
replies
590
views
Job:
Bioinformatics PhD: The circadian clock in the ageing plant, University of York, UK
transcriptomics
gene expression
time series
plant biology
circadian
Job
3.6 years ago
dezer
▴ 10
2
votes
2
replies
1.7k
views
How adjusted p-values are calculated in limma
limma
r
transcriptomics
FDR
statistics
updated 3.7 years ago by
Gordon Smyth
47k • written 3.7 years ago by
Wuschel
▴ 10
2
votes
0
replies
2.0k
views
Job:
Bioconductor infrastructure for the integration of genomics, transcriptomics and proteomics data
proteomics
genomics
transcriptomics
software
Job
3.7 years ago
Laurent Gatto
1.6k
1
vote
1
reply
574
views
cpm filtering parameter
cpm filtering
transcriptomics
rnaseq
edgeR
metatranscriptomics
updated 3.7 years ago by
Gordon Smyth
47k • written 3.7 years ago by
vm.higareda
▴ 10
0
votes
0
replies
683
views
Job:
Bionformatician Position / Heidelberg
neuroscience
data integration
transcriptomics
Job
4.2 years ago • updated 4.1 years ago
slezak
• 0
0
votes
0
replies
536
views
How to integrate and visualize RNASeq / Proteomics data for metabolomics pathways?
r
metabolomics
KEGG
Proteomics
Transcriptomics
4.2 years ago
Wuschel
▴ 10
1
vote
0
replies
1.3k
views
Job:
Full time and permanent research logistician in Bioinformatics
transcriptomics
proteomics
job
bioinformatician
Job
4.2 years ago
Laurent Gatto
1.6k
1
vote
0
replies
1.1k
views
News:
Bioinformatics Summer School - July 2019 - UCLouvain (Belgium)
RNAseq
deseq2
proteomics
transcriptomics
workshop
News
4.3 years ago
Laurent Gatto
1.6k
3
votes
4
replies
993
views
Writing a loop to clean up protein names
Proteomics
Transcriptomics
Loops
batch-processing
R
updated 4.6 years ago by
Sebastian Gibb
▴ 80 • written 4.6 years ago by
laural710
• 0
42 results • Page
1 of 1
Recent ...
Replies
Comment: Visualization of negative log CPM values
by
Gordon Smyth
47k
Sorry, but some of the things you say are not correct. > compound B has 2 statistically significant genes that are up-regulated No, there…
Comment: Visualization of negative log CPM values
by
ATpoint
★ 2.8k
Applies to both.
Comment: Visualization of negative log CPM values
by
Sabiha
▴ 10
@atpoint OK, are you referring to the `log2(cpm+1)` or `log2(tpm+1)`
Comment: Visualization of negative log CPM values
by
Sabiha
▴ 10
@gordonsmyth noted. Related to the graphs above, the table below is the output from `limma`, and compound B has 2 statistically significant…
Comment: Visualization of negative log CPM values
by
Gordon Smyth
47k
> negative scale might perhaps indicate gene is too low to be really expressed. Yes, negative logCPMs do mean that the gene is expressed a…
Votes
Comment: Visualization of negative log CPM values
Any efficient workaround to identify highly variable genes in Affymetrix microarray expression data?
Filtering low intensity probes in microarray data
Comment: Visualization of negative log CPM values
Adjusting for baseline when having longitudinal data, mixed model and no treatment
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