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970 results • Page
2 of 20
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Views
Votes
Replies
3
votes
2
replies
5.2k
views
RNASeq: Differential gene expression and qqplot
limma
differential-gene-expression
RNA-Seq
deseq2
updated 26 days ago by
Ram
43k • written 6.2 years ago by
firestar
★ 1.6k
2
votes
7
replies
5.1k
views
9 follow
problem with HOMER findMotifsGenome.pl
HOMER
ATAC-Seq
updated 25 days ago by
kaaz
• 0 • written 5.6 years ago by
ste.lu
▴ 80
1
vote
7
replies
5.1k
views
How do I plot several sns.clustermap heatmaps in a single figure?
python
seaborn
updated 25 days ago by
Wubin
▴ 40 • written 3.5 years ago by
roy.granit
▴ 880
0
votes
1
reply
5.0k
views
How to compute a one tail (one way) log rank test for survival?
R
survival
hypothesis-testing
log-rank
updated 25 days ago by
jack
• 0 • written 7.6 years ago by
denalitastic
▴ 30
3
votes
8
replies
5.0k
views
An idea to identify batch effects
microarray
batch-effect
updated 17 days ago by
Ram
43k • written 9.7 years ago by
mjarosz
• 0
23
votes
11
replies
4.9k
views
7 follow
Code golf: detecting homopolymers of length N in the (human) genome
code golf
fasta
homopolymer
repeat
updated 20 days ago by
Ram
43k • written 5.0 years ago by
WouterDeCoster
47k
1
vote
9
replies
4.7k
views
Help with multiple batch effects
sva
combat
batch-effect
updated 19 days ago by
Ram
43k • written 5.9 years ago by
fp89
▴ 30
1
vote
2
replies
4.6k
views
predict TF binding sites from DNA sequence
TF
TRANSFAC
TFBS
binding-site
updated 19 days ago by
Ram
43k • written 6.7 years ago by
grant.hovhannisyan
★ 2.6k
7
votes
3
replies
4.6k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA
RNA-Seq
batch-effect
updated 18 days ago by
Ram
43k • written 5.1 years ago by
tujuchuanli
▴ 100
4
votes
7
replies
4.6k
views
snakemake output directory
snakemake
ngs
updated 20 days ago by
进
• 0 • written 3.9 years ago by
Peter Chung
▴ 200
2
votes
4
replies
4.5k
views
Differential Expression Analysis with monocle and batch effect correction
single-cell
RNA-Seq
batch-effect
updated 18 days ago by
Ram
43k • written 6.0 years ago by
Poorya Parvizi
▴ 60
9
votes
10
replies
4.4k
views
Using rnaseq reference sample across batches
RNA-Seq
batch-effect
updated 19 days ago by
Ram
43k • written 7.4 years ago by
denalitastic
▴ 30
12
votes
13
replies
4.4k
views
RNA-Seq DGE using PCA components as covariate
differential-gene-expression
RNA-Seq
glm
DESeq2
updated 26 days ago by
Ram
43k • written 6.2 years ago by
firestar
★ 1.6k
18
votes
20
replies
4.4k
views
6 follow
How to identify significant differentially expressed genes and gene regulatory networks from microarray data.
microarray
differential-gene-expression
updated 26 days ago by
Ram
43k • written 7.6 years ago by
morteza.mahmoudisaber
▴ 80
6
votes
6
replies
4.4k
views
10x to cloupe
single-cell-transcriptomics
10x
27 days ago by
firestar
★ 1.6k
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 26 days ago by
Ram
43k • written 5.0 years ago by
RNAseqer
▴ 270
5
votes
20
replies
4.2k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression
RNA-seq
updated 26 days ago by
Ram
43k • written 6.2 years ago by
pablo61991
▴ 90
3
votes
2
replies
4.2k
views
Batch effects in sequencing data
batch-effect
updated 17 days ago by
Ram
43k • written 8.7 years ago by
Andrew
▴ 60
3
votes
8
replies
4.2k
views
Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
fpkm
scRNA-seq
RNA-Seq
tpm
batch-effect
updated 17 days ago by
Ram
43k • written 4.6 years ago by
hkarakurt
▴ 180
9
votes
12
replies
4.1k
views
Batch effect, how to create a model matrix
RNA-Seq
deseq2
batch-effect
updated 18 days ago by
Ram
43k • written 5.0 years ago by
Mozart
▴ 330
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 17 days ago by
Ram
43k • written 7.7 years ago by
Lluís R.
★ 1.2k
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression
Salmon
updated 26 days ago by
Ram
43k • written 5.6 years ago by
lkianmehr
▴ 100
3
votes
6
replies
4.0k
views
Loading previously downloaded GEO SOfT data into R, using getGEO from GEOquery package
microarray
r
GEOquery
updated 19 days ago by
Ram
43k • written 5.0 years ago by
mosesoo
▴ 30
1
vote
10
replies
4.0k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 22 days ago by
Aspire
▴ 330 • written 19 months ago by
Manav
• 0
4
votes
6
replies
3.9k
views
Correcting for batch effect in RNA-seq data
RNA-Seq
batch-effect
updated 18 days ago by
Ram
43k • written 4.8 years ago by
Rimma
▴ 30
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 6 days ago by
Andres
▴ 20 • written 9.6 years ago by
hermathena
▴ 40
3
votes
4
replies
3.8k
views
Error in ComBat function: Error in dat[, batch == batch_level] : (subscript) logical subscript too long
Batch-effect
microarray
R
updated 19 days ago by
Ram
43k • written 2.9 years ago by
Sib
▴ 60
30
votes
12
replies
3.8k
views
Trying to understand the maths behind one Limma function
limma
RNA-Seq
batch-effect
updated 20 days ago by
Ram
43k • written 4.0 years ago by
Mozart
▴ 330
4
votes
2
replies
3.8k
views
DESeq2 design and batch effect
RNA-Seq
batch-effect
DESeq2
Salmon
updated 17 days ago by
Ram
43k • written 6.5 years ago by
georgewwp
▴ 30
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 2 hours ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
25
votes
11
replies
3.7k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 12 days ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
2
votes
6
replies
3.7k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell
RNAseq
DE Analysis
Treatment
Control
updated 10 days ago by
ATpoint
82k • written 3.9 years ago by
grayapply2009
▴ 280
2
votes
6
replies
3.7k
views
Algorithm to remove batch effects
single-cell
batch-effect
RNA-Seq
updated 19 days ago by
Ram
43k • written 3.3 years ago by
fouerghi20
▴ 80
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 26 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
7
votes
2
replies
3.7k
views
Timeout on getBM() to retrieve snps from locations
biomaRt
getBM
R
updated 19 days ago by
Ram
43k • written 5.2 years ago by
Corentin
▴ 600
1
vote
3
replies
3.6k
views
Does Harmony batch correction for scRNA-seq require the same populations to be present in all samples?
Harmony
single-cell
scRNA-seq
batch-effect
updated 17 days ago by
Ram
43k • written 4.6 years ago by
Lucy
▴ 140
0
votes
13
replies
3.6k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 12 days ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
3
votes
4
replies
3.5k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 17 days ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
1
vote
8
replies
3.5k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 18 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 19 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
4
votes
5
replies
3.4k
views
Please clarify me about countOverlaps()?
RNA-Seq
countOverlaps
R
updated 19 days ago by
Ram
43k • written 6.3 years ago by
seta
★ 1.9k
1
vote
3
replies
3.4k
views
How to correct for batch effect in microarray meta-analysis
ComBat
microarray
meta-analysis
batch-effect
updated 17 days ago by
Ram
43k • written 10.0 years ago by
BrunoGiotti
▴ 120
6
votes
11
replies
3.4k
views
Collapsing probesets to genes on WGCNA
WGCNA
gene-expression
R
updated 19 days ago by
Ram
43k • written 5.3 years ago by
Davide Chicco
▴ 120
3
votes
4
replies
3.3k
views
Motif analysis of DMRs (Differentially Methylated Regions) by HOMER
next-gen
updated 25 days ago by
Ram
43k • written 6.7 years ago by
inschigu
▴ 10
1
vote
3
replies
3.3k
views
How to calculate Differential Gene expression between samples with replicates
Differential-Gene-Expression
RNA-Seq
updated 26 days ago by
Ram
43k • written 7.9 years ago by
doncheng1
• 0
0
votes
3
replies
3.2k
views
Batch correction (mass spectrometry data)
Combat
R
SVA
Biostatistics
batch-effect
updated 17 days ago by
Ram
43k • written 7.5 years ago by
mkhadka10
• 0
0
votes
1
reply
3.2k
views
Removing batch effects from RPKM data
limma
removeBatchEffect
batch-effect
rpkm
updated 19 days ago by
Ram
43k • written 8.5 years ago by
AB
▴ 360
1
vote
4
replies
3.2k
views
remove batch effect for multiple tumor data
RNA-Seq
batch-effect
updated 17 days ago by
Ram
43k • written 7.1 years ago by
hellocita
▴ 40
2
votes
1
reply
3.1k
views
Batch effect correction in DE analysis of single cell RNA-seq data and visualization
Seurat
Batch-effect
SCDE
RNA-Seq
Limma
updated 18 days ago by
Ram
43k • written 5.5 years ago by
Poorya Parvizi
▴ 60
0
votes
3
replies
3.1k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 17 days ago by
Ram
43k • written 9.0 years ago by
siddharth.patel.153
• 0
970 results • Page
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I assume that all data are from the same experiment, without batch effects and can thus be quantitiatively compared: Many ways to do thi…
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