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RNAseq
•
reset
5
votes
6
replies
2.1k
views
Improving the performance of the align function from Rsubread for old Roche454 reads
align
rsubread
roche454
rnaseq
updated 6.5 years ago by
Wei Shi
★ 3.6k • written 6.5 years ago by
Raito92
▴ 60
0
votes
3
replies
1.2k
views
Differential gene expression of time series RNAseq expermimnet with one cohort (diseased)
RNASeq
Timeseries experiment
updated 6.5 years ago by
James W. MacDonald
68k • written 6.5 years ago by
pbachali
▴ 50
3
votes
3
replies
1.9k
views
Recount data for unannotated genes
recount
RNAseq
gencode
lncRNA
gene annotation
updated 6.5 years ago by
chris.wilks
▴ 70 • written 6.6 years ago by
francesco.gandolfi
▴ 20
0
votes
0
replies
1.1k
views
Job:
Data science research assistant position at Johns Hopkins
RNAseq
R
Next-Gen Sequencing
Imaging
Brain
Job
6.5 years ago
hjaarop1
• 0
7
votes
5
replies
5.1k
views
featureCounts returning a matrix of counts full of 0...
featureCounts
rnaseq
Rsubread
updated 6.5 years ago by
Gordon Smyth
53k • written 6.5 years ago by
Raito92
▴ 60
1
vote
1
reply
1.4k
views
How to normalize RNA-seq when 50% genes are DE? (TMM)
limma
TMM
differential expression
normalization
rnaseq
updated 6.5 years ago by
James W. MacDonald
68k • written 6.5 years ago by
natalia_lt
• 0
1
vote
6
replies
7.4k
views
GSVA on RNAseq data
gsva
rnaseq
updated 8 months ago by
Robert Castelo
★ 3.4k • written 6.5 years ago by
rocanja
▴ 60
1
vote
3
replies
2.4k
views
DESeq2 log2FoldChange is very large and differs strongly from manually calculated.
deseq2
RNAseq
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
Matthias Munz
▴ 20
1
vote
9
replies
3.5k
views
error in aSwitchlist (isoformswitchanalyzeR)
isoformswitchanalyzeR
tximport
rnaseq
salmon
updated 6.5 years ago by
k.vitting.seerup
▴ 120 • written 6.5 years ago by
saddamhusain77
• 0
0
votes
0
replies
975
views
Paired DE analysis in edgeR with trios of samples while blocking for various confounders
edger
rnaseq
paired analysis
design matrix
6.5 years ago
svlachavas
▴ 840
2
votes
17
replies
3.7k
views
Computationally Singular Matrices - DESeq
deseq2
rnaseq
sva
updated 2.9 years ago by
Michael Love
43k • written 6.5 years ago by
flippy23
• 0
1
vote
3
replies
1.4k
views
Deseq2 polysome profiling analysis
deseq2
rnaseq
updated 6.6 years ago by
Michael Love
43k • written 6.6 years ago by
irene.diaz
▴ 10
0
votes
0
replies
1.4k
views
TCGAbiolinks specific mutation query
TCGAbiolinks
TCGA
Mutation
GDCquery
rnaseq
6.6 years ago
Yonatan Amzaleg
• 0
0
votes
0
replies
1.0k
views
removing confounding batch efffect with RUVg
RUVg
RNAseq
batch effect
6.6 years ago
gtechbio
▴ 10
5
votes
4
replies
1.8k
views
Foldchange values Limma
limma
RNAseq
foldchange
6.6 years ago
susana.amaral.teixeira
▴ 20
1
vote
3
replies
1.7k
views
Error using Conditional Quartile Normalization (CQN)
RNAseq
normalization
CQN
conditionalquartilenormalization
debugging
updated 6.6 years ago by
Kasper Daniel Hansen
★ 6.5k • written 6.6 years ago by
garbuzov
• 0
3
votes
7
replies
30k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2
gsea
rnaseq
gene espression
updated 6.6 years ago by
Michael Love
43k • written 6.6 years ago by
bmreilly
• 0
1
vote
1
reply
1.8k
views
News:
Bioinformatics Summer School - July 2019 - UCLouvain (Belgium)
RNAseq
deseq2
proteomics
transcriptomics
workshop
News
written 6.6 years ago by
Laurent Gatto
1.6k
0
votes
1
reply
1.4k
views
Deseq2 padjusted values versus pvalue
deseq2
RNASeq
padjusted
updated 6.6 years ago by
Michael Love
43k • written 6.6 years ago by
tanyabioinfo
▴ 30
0
votes
2
replies
1.0k
views
biomart not ound some prevous release
biomart
rnaseq
written 6.6 years ago by
jarod_v6@libero.it
▴ 40
8
votes
4
replies
3.3k
views
edgeR /DESeq2 normalization for differential expression in RNA-seq blood samples
hemoglobin
edgeR
deseq2
normalization
rnaseq
updated 6.7 years ago by
Ryan C. Thompson
★ 7.9k • written 6.7 years ago by
aec
▴ 90
1
vote
3
replies
797
views
How do you obtain the R - squared value from the NB line produced in plotMeanVar ?
edger
rnaseq
R
updated 6.7 years ago by
Gordon Smyth
53k • written 6.7 years ago by
nickwongga
• 0
0
votes
1
reply
1.7k
views
glm.fit problem with maSigPro
software error
maSigPro
Nueda
RNAseq
updated 6.7 years ago by
James W. MacDonald
68k • written 6.7 years ago by
lalamig
• 0
1
vote
1
reply
612
views
Script for fold change in DESeq for count data with 2 groups
deseq2
RNAseq
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
marc.osullivan
• 0
0
votes
1
reply
612
views
Deseq2 two controls in design experiment
Deseq2
RNASeq
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
tanyabioinfo
▴ 30
0
votes
9
replies
17k
views
How to generate a volcano plot when p-values from DESeq2 are zero?
deseq2
pvalue
visualization
enhancedvolcano
rnaseq
written 6.7 years ago by
ricardo3889
• 0
1
vote
2
replies
1.3k
views
Meta-analysis of RNAseq data
RNAseq
meta-analysis
microarray
public data sets
updated 6.7 years ago by
alexvpickering
▴ 110 • written 6.7 years ago by
Vladimir Krasikov
▴ 90
2
votes
3
replies
1.3k
views
Batch correction for a sets of genes
cancer
deseq2
r
rnaseq
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
AZ
▴ 30
0
votes
3
replies
1.2k
views
Is it allowed to fit two models to make between and within subjects comparisons separately?
rnaseq
limma
edger
deseq2
random effects
6.7 years ago
tcalvo
▴ 100
2
votes
2
replies
2.1k
views
Different DEG results using Ballgown and edgeR
edger
ballgown
rnaseq
batch effect
adjustvars
updated 6.7 years ago by
Gordon Smyth
53k • written 6.7 years ago by
IRAIA.MAIALEN
• 0
1
vote
2
replies
1.4k
views
Aclaration of batch effect adjust in DE analysis
edger
rnaseq
batch effect
updated 6.8 years ago by
James W. MacDonald
68k • written 6.8 years ago by
IRAIA.MAIALEN
• 0
0
votes
0
replies
1.4k
views
Tumor subtype classification when genes of gene set are missing from samples - GSVA approach
GSVA
geneset
RNASeq
TCGA
subtypes
6.8 years ago
Pietro
▴ 40
4
votes
1
reply
1.8k
views
Data preparation and Machine learning on time course RNAseq data
machine learning
deep learning
RNAseq
MLSeq
6.8 years ago
A
▴ 60
0
votes
3
replies
2.4k
views
Uncertain about PCA plot for DESeq2 analysis
deseq2
pca
bioconductor
rnaseq
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
pepere
▴ 40
12
votes
12
replies
3.2k
views
FDR does not change between genes in edgeR
RNAseq
edgeR
updated 6.8 years ago by
Gordon Smyth
53k • written 6.8 years ago by
apfelbapfel
▴ 30
0
votes
1
reply
601
views
Unusual DESeq2 results
deseq2
rnaseq
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
taamslab
• 0
1
vote
3
replies
1.8k
views
how to find expressed genes in RNAseq
deseq2
rnaseq
differential gene expression
featurecounts
rnaseqGene
6.8 years ago
melkile26
• 0
0
votes
2
replies
2.4k
views
How can I compare the expression of two genes within the same sample?
gene expression
rnaseq
deseq2
updated 6.8 years ago by
heyao
▴ 30 • written 6.8 years ago by
chiara.facciotto
• 0
5
votes
1
reply
5.9k
views
RNAseq analysis: what comes first, filtering or normalization
edger
R
rnaseq
updated 6.8 years ago by
Aaron Lun
★ 29k • written 6.8 years ago by
apfelbapfel
▴ 30
1
vote
8
replies
2.1k
views
DESeq2 model design for paired samples with multiple factors
deseq2
rnaseq
model design
6.8 years ago
swillis4
▴ 10
1
vote
1
reply
1.4k
views
tximport of 3 tagged RNA-seq counts from Salmon for downstream analysis with DESeq2
tximport
deseq2
rnaseq
3' tagged RNA
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
rbenel
▴ 50
0
votes
1
reply
3.3k
views
Deconvolution Method in Seurat and convert from SingleCellExperiment
scater
seurat
singlecellexperiment
rnaseq
updated 6.8 years ago by
Gordon Smyth
53k • written 6.8 years ago by
hamza_karakurt
▴ 60
6
votes
14
replies
3.0k
views
Help analyzing RNA-seq data from FPKM values with multiple time points
rnaseq
limma
updated 6.8 years ago by
Aaron Lun
★ 29k • written 6.8 years ago by
rsrzkk
• 0
2
votes
1
reply
979
views
Help with multi-factored RNA-seq edgeR model
edger
design model
interaction model
rnaseq
updated 6.8 years ago by
James W. MacDonald
68k • written 6.8 years ago by
cody0071
• 0
0
votes
3
replies
3.9k
views
Issue with DESeqDataSetFromMatrix
deseq2
deseqdatasetfrommatrix
rnaseq
affy
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
matthew.sinton
• 0
0
votes
1
reply
1.1k
views
DGE Analysis between 3 conditions
deseq2
rnaseq
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
evocanres
• 0
2
votes
3
replies
2.6k
views
DESeq2 count outlier replacement from Cook's threshold
deseq2
deseq
rnaseq
outliers
count outliers
updated 6.9 years ago by
Michael Love
43k • written 6.9 years ago by
lefeverde
▴ 10
1
vote
1
reply
754
views
how to retrieve gene id from topGO results
rnaseq
6.9 years ago
ycding
▴ 20
0
votes
3
replies
4.5k
views
Data normalization and transformation using DESeq2
deseq2
normalization
rnaseq
rlog transformation
variancestabilizingtransformation
6.9 years ago
chiara.facciotto
• 0
3
votes
6
replies
2.8k
views
Controlling numerical covariates: differential gene expression with limma voom
limma
voom
differential gene expression
rnaseq
R
updated 6.9 years ago by
mikhael.manurung
▴ 280 • written 6.9 years ago by
Onyi Ukay
• 0
1,409 results • Page
11 of 29
Recent ...
Replies
Comment: Help with defining groups
by
Phinney, Brett
▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness
by
massimo
• 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package
by
ksankaran
• 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
by
ATpoint
★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes
by
ATpoint
★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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