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Showing :
transcriptomics
•
reset
3
votes
2
replies
199
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
4 weeks ago
Anita
▴ 10
3
votes
5
replies
1.3k
views
DESeq2, time-course interpretation
Transcriptomics
TimeCourse
DESeq2
updated 9 months ago by
Michael Love
41k • written 9 months ago by
smac97
• 0
0
votes
4
replies
732
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor
Transcriptomics
DifferentialExpression
DESeq2
11 months ago
sreeshmaraj72
• 0
0
votes
1
reply
343
views
Time change in expression vs time change in phenotype
Transcriptomics
ExpressionData
DESeq2
updated 12 months ago by
Michael Love
41k • written 12 months ago by
Ivan
• 0
4
votes
5
replies
1.6k
views
EnhancedVolcano - Unable to customize the length of Connectors to Gene Labels
Transcriptomics
EnhancedVolcano
updated 12 months ago by
Kevin Blighe
★ 3.9k • written 12 months ago by
Peter
▴ 20
4
votes
8
replies
1.3k
views
DESEQ2 - What is the recommended workflow in terms of pre-filtering and counts normalization?
DESeq2
Transcriptomics
updated 12 months ago by
Wolfgang Huber
★ 13k • written 12 months ago by
Peter
▴ 20
0
votes
3
replies
732
views
Understanding edgeR differential expression results
Transcriptomics
edgeR
DifferentialExpression
RNASeqData
RNASeq
updated 14 months ago by
Gordon Smyth
50k • written 14 months ago by
Teresa
• 0
0
votes
1
reply
711
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 15 months ago by
Dario Strbenac
★ 1.5k • written 15 months ago by
Hicham
▴ 10
0
votes
1
reply
1.2k
views
Variance stabilization transformation (VST), blind=TRUE
DESeq2
Transcriptomics
RNASeq
updated 15 months ago by
Michael Love
41k • written 15 months ago by
Jayesh Kumar
• 0
0
votes
0
replies
523
views
EdgeR without replication
Transcriptomics
16 months ago
kuttibiotech2009
• 0
0
votes
0
replies
542
views
Analysis of TIF-seq data to generate transcription start sites (TSS) and poly(A) site (PAS) clusters
Transcriptomics
SequencingData
17 months ago
Rom
• 0
0
votes
0
replies
589
views
Job:
EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq
Transcriptomics
Pathways
Epigenetics
RNASeq
17 months ago
whduke
• 0
0
votes
2
replies
682
views
Questions about `collapseReplicates` function in DESeq2
DESeq2
Transcriptomics
18 months ago
Yijing
• 0
0
votes
0
replies
514
views
WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network
Transcriptomics
MicrobiomeData
RNASEQ
WCGNA
19 months ago
Julieta
• 0
2
votes
1
reply
1.5k
views
Understanding tximport working with salmon outputs
Transcriptomics
tximport
updated 19 months ago by
ATpoint
★ 4.0k • written 19 months ago by
Florent
▴ 10
0
votes
3
replies
962
views
DESeq2 - transcript length correction necessary when quantifying reads from ends of transcripts?
Transcriptomics
DESeq2
21 months ago
marius.wenzel
• 0
4
votes
6
replies
1.4k
views
How to best visualize multi-level transcriptomics experiment data?
ggplot2
Transcriptomics
Visualization
R
limma
23 months ago
mohammedtoufiq91
▴ 10
1
vote
3
replies
1.0k
views
Identifying DEG between development stages
plant
Transcriptomics
DESeq2
r
updated 2.1 years ago by
Basti
▴ 780 • written 2.1 years ago by
cicely.day
• 0
2
votes
5
replies
1.4k
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
807
views
Deseq2 Resul variation by LFC variation
rnaseqGene
DESeq2
Transcriptomics
2.5 years ago • updated 11 months ago
diangomaiga
• 0
1
vote
2
replies
1.3k
views
Not many DE genes using glmTreat
EdgeR
Bioinformatics
Transcriptomics
Quantseq
2.7 years ago
Barista
• 0
0
votes
0
replies
898
views
Job:
Senior Bioinformatician - University of Alabama at Birmingham
JobPosting
Transcriptomics
SingleCell
RNA-seq
2.7 years ago
lianov
• 0
0
votes
0
replies
816
views
Job:
[apply by 8/15] PhD scholarship on functional and evolutionary genomics
JobPosting
Transcriptomics
GenomicVariation
2.8 years ago
marie
• 0
0
votes
2
replies
942
views
Downloading org.Mm.eg.db after R reinstall
org.Mmu.eg.db
Transcriptomics
3.0 years ago
Kate
• 0
0
votes
0
replies
922
views
Consensus wgcna soft threshold for each data
Transcriptomics
WGCNA
wgcna
3.1 years ago
2323982403
▴ 60
0
votes
1
reply
753
views
Metatranscriptomics DESeq2 multifactorial sampling
Transcriptomics
DESeq2
updated 3.1 years ago by
Michael Love
41k • written 3.1 years ago by
seppe.demits
• 0
0
votes
0
replies
934
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 3.2 years ago by
James W. MacDonald
65k • written 3.2 years ago by
H. Z. Amini
▴ 10
0
votes
0
replies
926
views
Job:
Computational Biologist at Denali Therapeutics
Transcriptomics
SingleCell
JobPosting
3.3 years ago
Steve Lianoglou
★ 13k
1
vote
1
reply
892
views
NanoStringDiff Not Recognized as Numeric
Bioconductor
Transcriptomics
NanoStringDiff
updated 3.5 years ago by
Laurent Gatto
1.6k • written 3.5 years ago by
Pedro
▴ 10
0
votes
0
replies
689
views
Problems with cummeRbund
plot
transcriptomics
differential expression
cummeRbund
4.1 years ago
raquelponti
• 0
1
vote
0
replies
951
views
News:
News: Bioinformatics Summer School - July 2020 - UCLouvain (Belgium)
rnaseq
course
proteomics
transcriptomics
scrnaseq
News
4.2 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
864
views
Job:
Bioinformatics Scientist, CNS Transcriptomics at Alnylam Pharmaceuticals, Cambridge MA, USA
scRNA-seq
CNS
transcriptomics
RNAi
Job
4.3 years ago
Joseph Barry
▴ 10
0
votes
0
replies
764
views
Job:
Bionformatician in personalized oncotherapy (BEL)
job
bioinformatician
immunotherapy
genomics
transcriptomics
Job
4.4 years ago
cedric
• 0
1
vote
0
replies
857
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
2.8k
views
How adjusted p-values are calculated in limma
limma
r
transcriptomics
FDR
statistics
updated 4.6 years ago by
Gordon Smyth
50k • written 4.6 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
4.6 years ago
Laurent Gatto
1.6k
1
vote
1
reply
913
views
cpm filtering parameter
cpm filtering
transcriptomics
rnaseq
edgeR
metatranscriptomics
updated 4.6 years ago by
Gordon Smyth
50k • written 4.6 years ago by
vm.higareda
▴ 10
0
votes
0
replies
921
views
Job:
Bionformatician Position / Heidelberg
neuroscience
data integration
transcriptomics
Job
5.1 years ago • updated 5.0 years ago
slezak
• 0
0
votes
0
replies
774
views
How to integrate and visualize RNASeq / Proteomics data for metabolomics pathways?
r
metabolomics
KEGG
Proteomics
Transcriptomics
5.1 years ago
Wuschel
▴ 10
1
vote
0
replies
1.6k
views
Job:
Full time and permanent research logistician in Bioinformatics
transcriptomics
proteomics
job
bioinformatician
Job
5.2 years ago • updated 5.1 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 5.2 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: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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