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1,114 results • Page
2 of 23
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Views
Votes
Replies
0
votes
7
replies
6.0k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq
WGCNA
removeBatchEffect
DESeq2
updated 9 days ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
3
votes
11
replies
6.0k
views
Modifying R pairs() function
plotMEpairs
WGCNA
R
updated 9 days ago by
Ram
43k • written 6.4 years ago by
shania90.lk
▴ 30
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 1 day ago by
rohitsatyam102
▴ 850 • written 6.1 years ago by
smallfish
▴ 10
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 6 days ago by
ndm1096
• 0 • written 6.5 years ago by
ac.research
▴ 30
10
votes
36
replies
5.8k
views
Design in DESeq: Can you combine explicit and implicit batch effect correction in (SVA+Metadata Variables)?
SVA
batch-effect
DESeq2
R
updated 9 days ago by
Ram
43k • written 5.7 years ago by
Kristin Muench
▴ 620
2
votes
7
replies
5.7k
views
8 follow
How to access specifically 30x NA12878 sequencing runs
giab
benchmark
fastq
wgs
data-access
updated 24 days ago by
geocarvalho
▴ 360 • written 5.1 years ago by
Fungsten
• 0
9
votes
8
replies
5.6k
views
7 follow
CONTRA for CNV detection. troubleshooting
genome
next-gen-sequencing
cnv
software-error
updated 29 days ago by
Ram
43k • written 9.9 years ago by
Kizuna
▴ 870
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 17 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
2
votes
7
replies
5.3k
views
6 follow
Memory usage of picard Samsort
Picard
SortSam
updated 7 days ago by
ATpoint
82k • written 7.2 years ago by
boymin2020
▴ 80
3
votes
2
replies
5.2k
views
RNASeq: Differential gene expression and qqplot
limma
differential-gene-expression
RNA-Seq
deseq2
updated 17 days ago by
Ram
43k • written 6.2 years ago by
firestar
★ 1.6k
8
votes
5
replies
5.2k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by
a.beggs
▴ 60
2
votes
6
replies
5.2k
views
How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq?
scRNA-seq
R
seurat
harmony
batch-effect
updated 8 days ago by
Ram
43k • written 3.7 years ago by
Lukadon77
• 0
2
votes
3
replies
5.1k
views
BLAST Ring Image Generator (BRIG) error
error
software
alignment
updated 23 days ago by
GenoMax
141k • written 7.4 years ago by
casley_queiroz
▴ 20
2
votes
7
replies
5.1k
views
9 follow
problem with HOMER findMotifsGenome.pl
HOMER
ATAC-Seq
updated 15 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 16 days ago by
Wubin
▴ 40 • written 3.4 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 15 days ago by
jack
• 0 • written 7.5 years ago by
denalitastic
▴ 30
3
votes
8
replies
4.9k
views
An idea to identify batch effects
microarray
batch-effect
updated 8 days ago by
Ram
43k • written 9.7 years ago by
mjarosz
• 0
23
votes
11
replies
4.8k
views
7 follow
Code golf: detecting homopolymers of length N in the (human) genome
code golf
fasta
homopolymer
repeat
updated 10 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 9 days ago by
Ram
43k • written 5.8 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 10 days ago by
Ram
43k • written 6.6 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 9 days ago by
Ram
43k • written 5.1 years ago by
tujuchuanli
▴ 100
4
votes
7
replies
4.5k
views
snakemake output directory
snakemake
ngs
updated 10 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 9 days ago by
Ram
43k • written 5.9 years ago by
Poorya Parvizi
▴ 60
9
votes
10
replies
4.4k
views
Using rnaseq reference sample across batches
RNA-Seq
batch-effect
updated 9 days ago by
Ram
43k • written 7.4 years ago by
denalitastic
▴ 30
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 17 days ago by
Ram
43k • written 7.5 years ago by
morteza.mahmoudisaber
▴ 80
12
votes
13
replies
4.4k
views
RNA-Seq DGE using PCA components as covariate
differential-gene-expression
RNA-Seq
glm
DESeq2
updated 17 days ago by
Ram
43k • written 6.2 years ago by
firestar
★ 1.6k
6
votes
6
replies
4.4k
views
10x to cloupe
single-cell-transcriptomics
10x
17 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 17 days ago by
Ram
43k • written 5.0 years ago by
RNAseqer
▴ 260
5
votes
20
replies
4.2k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression
RNA-seq
updated 17 days ago by
Ram
43k • written 6.2 years ago by
pablo61991
▴ 90
3
votes
2
replies
4.1k
views
Batch effects in sequencing data
batch-effect
updated 8 days ago by
Ram
43k • written 8.7 years ago by
Andrew
▴ 60
3
votes
8
replies
4.1k
views
Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
fpkm
scRNA-seq
RNA-Seq
tpm
batch-effect
updated 8 days ago by
Ram
43k • written 4.6 years ago by
hkarakurt
▴ 180
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 8 days ago by
Ram
43k • written 7.6 years ago by
Lluís R.
★ 1.2k
9
votes
12
replies
4.1k
views
Batch effect, how to create a model matrix
RNA-Seq
deseq2
batch-effect
updated 9 days ago by
Ram
43k • written 4.9 years ago by
Mozart
▴ 330
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression
Salmon
updated 17 days ago by
Ram
43k • written 5.5 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 9 days ago by
Ram
43k • written 5.0 years ago by
mosesoo
▴ 30
4
votes
6
replies
3.9k
views
Correcting for batch effect in RNA-seq data
RNA-Seq
batch-effect
updated 9 days ago by
Ram
43k • written 4.8 years ago by
Rimma
▴ 30
1
vote
10
replies
3.9k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 12 days ago by
Aspire
▴ 300 • written 18 months ago by
Manav
• 0
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 10 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 11 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 8 days ago by
Ram
43k • written 6.5 years ago by
georgewwp
▴ 30
25
votes
11
replies
3.7k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 3 days ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
1
vote
3
replies
3.7k
views
MSF Data Analysis
MSF
Proteomics
Thermo
Proteome Discoverer
updated 22 days ago by
iqra
• 0 • written 4.4 years ago by
JJDollar
▴ 130
2
votes
6
replies
3.7k
views
Algorithm to remove batch effects
single-cell
batch-effect
RNA-Seq
updated 10 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 17 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 9 days ago by
Ram
43k • written 5.2 years ago by
Corentin
▴ 600
2
votes
6
replies
3.6k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell
RNAseq
DE Analysis
Treatment
Control
updated 1 day ago by
ATpoint
82k • written 3.9 years ago by
grayapply2009
▴ 280
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 8 days ago by
Ram
43k • written 4.5 years ago by
Lucy
▴ 140
8
votes
12
replies
3.5k
views
Why should ATAC-seq mapped reads be shifted +4 and -5 for +strand and -strand, respectively
ATAC-seq
updated 23 days ago by
Maksim
• 0 • written 3.4 years ago by
progistar
▴ 40
0
votes
13
replies
3.5k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 2 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 8 days ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
1,114 results • Page
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Thank you Pierre! I'll try this out with my full data set.
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Check out clustergrammer from Avi Ma'ayan's lab.
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