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2
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1.7k
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feature reduction using machine learning
rnaseq
machine learning
feature selection
updated 7.2 years ago by
chris86
▴ 420 • written 7.2 years ago by
marak
• 0
0
votes
1
reply
1.6k
views
Pick coding vs non-coding from Ensembl data set
R
ensembl
ensembldb
noncoding rna
protein coding
updated 7.2 years ago by
Johannes Rainer
★ 2.1k • written 7.2 years ago by
jdmentze
• 0
1
vote
5
replies
1.6k
views
Biomart cannot get multiple genes?
R
biomart
7.2 years ago
Mike
▴ 10
2
votes
2
replies
2.6k
views
[MnnCorrect] Remove batch effects but keep condition effects
single-cell
scran
mnncorrect
rnaseq
updated 7.2 years ago by
Aaron Lun
★ 29k • written 7.2 years ago by
John Reid
▴ 10
8
votes
2
replies
1.8k
views
News:
BioCAsia, 29-30th November 2018, Melbourne, Australia
news
conference
training
News
updated 7.2 years ago by
Gordon Smyth
53k • written 7.4 years ago by
Steve Pederson
▴ 170
0
votes
2
replies
1.8k
views
GEOQuery bug, NCBI or package?
geoquery
ncbi geo
biobase
7.2 years ago
cschot3
• 0
1
vote
4
replies
1.9k
views
RNA-seq analysis using R
limma
rnaseq
convert
R
updated 2.8 years ago by
Gordon Smyth
53k • written 7.2 years ago by
justinkablan225
▴ 10
12
votes
4
replies
5.3k
views
WGCNA following salmon/DESeq2
deseq2
wgcna
salmon
updated 7.2 years ago by
Peter Langfelder
★ 3.0k • written 7.2 years ago by
maya.kappil
▴ 30
2
votes
3
replies
2.8k
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon
edaseq
rna-seq
deseq2
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
maya.kappil
▴ 30
0
votes
4
replies
2.8k
views
DESeq2 for Cut&Run and differential enrichment testing
deseq2
Cut&Run
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
MPerch
• 0
0
votes
2
replies
1.3k
views
getting the sequences of 3UTR and the gene names
GenomeFeatures
updated 7.2 years ago by
James W. MacDonald
68k • written 7.2 years ago by
Bogdan
▴ 670
2
votes
6
replies
2.8k
views
topGO: GO terms in gene annotation do not match significant GO term output
rnaseq
topgo
go enrichment
updated 7.2 years ago by
James W. MacDonald
68k • written 7.2 years ago by
jgg
• 0
0
votes
2
replies
1.5k
views
logfold shrinkage DESeq2
deseq2
7.2 years ago
sherajilir
• 0
0
votes
0
replies
1.3k
views
How to left or right align titles in Gviz tracks?
gviz
title
text formatting
grid
7.2 years ago
alex.gos90
▴ 10
0
votes
1
reply
2.0k
views
DESeq2 paired design with missing samples and multiple conditions
deseq2
paired samples
missing data
multiple treatments
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
greg.deakin
• 0
0
votes
1
reply
1.7k
views
rtracklayer::Problem with export.bw of GRanges object created by unlisted after liftover from mm9 to mm10 of wig file
rtracklayer
export.bw
liftover
updated 7.2 years ago by
Michael Lawrence
★ 11k • written 7.2 years ago by
ang
▴ 20
0
votes
2
replies
1.9k
views
MA plot scattering pattern
deseq2
MAplot
7.2 years ago
avitalwasser
• 0
0
votes
3
replies
1.4k
views
What does component or SCX classification in iTRAQ/TMT experiment represent?
proteomics
updated 7.2 years ago by
Laurent Gatto
1.6k • written 7.2 years ago by
larryhunt
• 0
0
votes
0
replies
1.4k
views
Query based on PMIDs
SRAdb
geoquery
7.2 years ago
Deepak Tanwar
▴ 10
1
vote
0
replies
1.5k
views
Job:
CRUK Cambridge Centre MRes + PhD in Cancer Biology (Cross-Programme Quantitative Projects)
PhD
cancer
deep learning
computational biology
Job
7.2 years ago
Shamith.Samarajiwa
▴ 180
3
votes
6
replies
3.6k
views
biomaRt: Ensembl -> Entrez conversion error?
biomart
entrez gene identifiers
ensembl
conversion
updated 7.2 years ago by
Mike Smith
★ 6.6k • written 7.2 years ago by
EdgeR_A_Poe
▴ 10
1
vote
1
reply
587
views
Do I have too many samples or are some samples causing issues?
deseq2
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
cmfield
• 0
0
votes
7
replies
2.1k
views
A problem with csaw that I don't think is a problem with csaw
csaw
caught segfault
7.2 years ago
sorjuelal
• 0
6
votes
7
replies
2.8k
views
Normalization for small non-coding RNA
TMM
deseq2
smallrna
rnaseq
updated 7.2 years ago by
António Miguel de Jesus Domingues
▴ 510 • written 7.2 years ago by
Konstantinos Yeles
▴ 90
6
votes
4
replies
2.9k
views
Limma Voom duplicateCorrelation Design
limma
voom
duplicatecorrelation
updated 7.2 years ago by
Aaron Lun
★ 29k • written 7.2 years ago by
bruce.moran
▴ 30
1
vote
0
replies
1.4k
views
Job:
applied methods development for single-cell sequencing
single-cell
job
computational biology
Job
7.2 years ago
Simon Anders
★ 3.8k
1
vote
2
replies
3.7k
views
How to convert bedgraph to wig
rtracklayer
genomicranges
updated 7.2 years ago by
Michael Lawrence
★ 11k • written 7.2 years ago by
ferbecneu
• 0
0
votes
5
replies
1.4k
views
GenomicFeatures supportedUCSCFeatureDbTracks never returns and has to be terminated with C-c
genomicfeatures
bug
updated 7.2 years ago by
James W. MacDonald
68k • written 7.2 years ago by
Malcolm Cook
★ 1.6k
0
votes
1
reply
1.6k
views
A recent update to readr cause issues loading data with GEOquery 2.50.0
version compatibility
bug
updated 7.2 years ago by
Steve Lianoglou
★ 13k • written 7.2 years ago by
stun24
• 0
0
votes
1
reply
784
views
DESeq2 on mixed species samples
deseq2
updated 7.2 years ago by
James W. MacDonald
68k • written 7.2 years ago by
swbarnes2
★ 1.4k
0
votes
1
reply
1.4k
views
Error when install bioconductor on Mac 10.12 Sierra
installation
updated 7.2 years ago by
Martin Morgan
25k • written 7.2 years ago by
thatwasfunny
• 0
14
votes
10
replies
5.0k
views
Error when trying to preprocessReads() : "Error: logical subscript contains NAs"
systempiper
7.2 years ago
Deleted
▴ 70
1
vote
1
reply
3.9k
views
Question regarding class imbalance and low sample size for DESeq2
deseq2
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
munna.uppal
• 0
0
votes
4
replies
1.8k
views
DESeq2 multifactor formula design
deseq2
time series
multiple factor design
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
Jane
• 0
0
votes
2
replies
1.8k
views
DESeq2 Design with Multiple Replicates of Individuals including Tumour and Normal
DESeq2
design and contrast matrix
7.2 years ago
bruce.moran
▴ 30
0
votes
0
replies
1.3k
views
ASpli Package: Problem with readCounts() function, no Junctions analysed.
rnaseq
alternative splicing
ASpli
7.2 years ago
nicolas.guyon2
• 0
1
vote
2
replies
1.2k
views
DESeq2 - assessing expression of low count genes
deseq2
HERVs
low counts
prefiltering
dispersion estimates
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
rodrigo.duarte88
▴ 40
0
votes
2
replies
3.9k
views
DESeq2 coefficients for APEGLM-shrinkage
deseq2
apeglm
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
zolotaryovgl
• 0
0
votes
1
reply
995
views
DESeq2 ratio of small p-values plot
deseq2
diagnostic plots
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
Nancy
▴ 10
1
vote
4
replies
1.8k
views
Problem with Upgrade to Bioconductor 3.8 on Scientific linux (CentOS) 7
upgrade
updated 7.2 years ago by
Martin Morgan
25k • written 7.2 years ago by
zacekm
▴ 10
0
votes
0
replies
1.5k
views
CAGEr get TSS in bed file
TSS
promoter
cage
cager
7.2 years ago
bharata1803
▴ 60
6
votes
10
replies
4.8k
views
edgeR paired samples with blocking
limma
edger
blocking
paired samples
updated 7.2 years ago by
Gordon Smyth
53k • written 7.2 years ago by
anou
▴ 10
2
votes
2
replies
1.6k
views
voom variance modeling: lowess curve fitting notation misunderstanding?
voom
updated 7.2 years ago by
Gordon Smyth
53k • written 7.2 years ago by
njbernstein
• 0
0
votes
1
reply
1.5k
views
STRINGdb: enrichment function raises error
STRINGdb
stringdb
gene set enrichment analysis
software error
go
7.2 years ago
wsciekly.maciek
▴ 10
4
votes
9
replies
4.2k
views
DESeq2 - Upgrade from 1.20.0 to 1.22.1 now gives warnings 'package:stats' may not be available when loading
deseq2
updated 7.2 years ago by
Martin Morgan
25k • written 7.2 years ago by
Benoit.Fiset
▴ 30
0
votes
3
replies
1.3k
views
Pairwise comparisons for "both between and within subject"experiment using DESeq2
pairwise
deseq2
extracting contrasts
resultsnames
results deseq2
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
Ricardo Rodrigues
• 0
2
votes
1
reply
1.9k
views
EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation
epic
champ
updated 7.2 years ago by
Yuan Tian
▴ 290 • written 7.2 years ago by
D
▴ 10
0
votes
3
replies
3.0k
views
DESeq2: removal of duplicated genes during statistical analysis
deseq2
gene symbol
ensembl
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
thkapell
▴ 10
1
vote
1
reply
1.3k
views
DEseq2 with different fastq read numbers after salmon
deseq2
salmon rna seq
salmon
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
danalvoronov
▴ 10
0
votes
1
reply
2.8k
views
converting mstrg labels from stringtie and prepDE.py to gene symbol for downstream biology
deseq2
updated 7.2 years ago by
Michael Love
43k • written 7.2 years ago by
harris
• 0
46,741 results • Page
238 of 935
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Comment: Upcoming Ensembl API and data access changes - new blog post available
by
Tikaaa2sahaaaq2c
• 0
Just as the Ensembl team transitions to a new platform for streamlined data access, diners can benefit from a digital newks menu prices con…
Comment: Error message that there is no package called Biobase
by
DamionLedner99
• 0
thanks for sharing!!! https://cran.r-project.org/
Comment: msmsTests, inconsistent sign between lFC.Av and LogFC
by
Ben
• 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis
by
James W. MacDonald
68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list'
by
varying.mastodon.isyn
• 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Votes
Answer: What happens to genes with low dispersion during dispersion shrinkage in DESeq2
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
A: DESeq2 normalization vs VST vs rlog
Answer: How to directly decet the outlier samples (libraries) in EdgeR pipeline
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