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158 results • Page
3 of 4
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
721
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq
scRNA-Seq
batch-effect
updated 12 hours ago by
Ram
43k • written 3.4 years ago by
hkarakurt
▴ 180
2
votes
0
replies
1.8k
views
ComBat-seq adjustment of batch effects
RNA-Seq
ComBat-seq
SVA
edgeR
batch-effect
updated 2 days ago by
Ram
43k • written 3.4 years ago by
chatterjee.arumoy
▴ 50
0
votes
1
reply
800
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR
Batch-effect
RNA-Seq
updated 13 hours ago by
Ram
43k • written 3.7 years ago by
jordan15
• 0
1
vote
6
replies
1.6k
views
How can Differentially Expressed Genes be found by limma package after removing batch effect by ComBat function in sva package?
limma
sva
batch-effect
R
updated 3 days ago by
Ram
43k • written 3.8 years ago by
amirmehrgou
▴ 10
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling
single-cell
scRNA-seq
batch-effect
updated 2 days ago by
Ram
43k • written 3.9 years ago by
jmah
▴ 20
0
votes
0
replies
1.2k
views
Batch estimate using kBET
batch-effect
kbet
updated 13 hours ago by
Ram
43k • written 4.0 years ago by
getanid123
• 0
0
votes
0
replies
724
views
"No group or design set" with deAna() function in EnrichmentBrowser package
RNA-Seq
R
EnrichmentBrowser
updated 2 days ago by
Ram
43k • written 4.1 years ago by
yxswhx
• 0
0
votes
0
replies
881
views
Advice on group specific condition effect and model matrix in deseq2
deseq2
batch-effect
updated 3 days ago by
Ram
43k • written 4.1 years ago by
Mozart
▴ 330
2
votes
3
replies
925
views
Possible approach to select normal tissue samples for cancer RNA-Seq data without reference data for downstream analyses
R
RNA-Seq
DE
batch-effect
GTEx
updated 3 days ago by
Ram
43k • written 4.1 years ago by
svlachavas
▴ 790
0
votes
3
replies
1.1k
views
Batch effect for SNP array
sva
combat
batch-effect
SNP
updated 3 days ago by
Ram
43k • written 4.2 years ago by
Taylor95
▴ 10
0
votes
0
replies
1.1k
views
Extra adjustment variables during batch effect correction
rna-seq
ComBat
batch-effect
updated 2 days ago by
Ram
43k • written 4.3 years ago by
n,n
▴ 360
0
votes
2
replies
1.0k
views
proportional hazard assumption was not satisfied for a covariate
hazard-ratios
Cox-model
survival
updated 2 days ago by
Ram
43k • written 4.3 years ago by
akutasame
▴ 40
1
vote
1
reply
652
views
Save experiment with batch effects - Protein microarray
statistics
protein-array
batch-effect
updated 2 days ago by
Ram
43k • written 4.4 years ago by
s.lima.diogenes
▴ 10
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq
batch-effect
DESeq2
updated 1 day ago by
Ram
43k • written 4.4 years ago by
baldissera152
▴ 10
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 1 day ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq
batch-effect
Random-Forest
updated 1 day ago by
Ram
43k • written 4.7 years ago by
Vlad
▴ 10
1
vote
8
replies
3.4k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 1 day ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
0
votes
1
reply
1.2k
views
Controlling for batch effect in SNP-based PCA
whole-genome
PCA
batch-effect
SNP
updated 1 day ago by
Ram
43k • written 4.7 years ago by
Ace
▴ 90
0
votes
4
replies
1.7k
views
Correcting batch effect in unevenly distributed groups
RNA-Seq
batch-effect
R
updated 1 day ago by
Ram
43k • written 4.8 years ago by
jperezboza
▴ 20
0
votes
1
reply
825
views
How to compare differentially expressed genes among different affymatrix dataset
microarray
batch-effect
R
updated 1 day ago by
Ram
43k • written 4.8 years ago by
Calangoa
▴ 30
1
vote
2
replies
1.7k
views
Batch effects and MDSPlot in limma
limma
Batch-effect
MDS
Galaxy
updated 2 days ago by
Ram
43k • written 4.8 years ago by
sonayuv
• 0
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect
omniexpress
GWAS
GSA
updated 1 day ago by
Ram
43k • written 4.8 years ago by
saksis.rihards
▴ 10
0
votes
0
replies
1.1k
views
Should batch correction be performed before or after feature selection in scRNA-seq
batch-effect
scRNA-seq
feature-selection
updated 1 day ago by
Ram
43k • written 4.9 years ago by
Lucy
▴ 140
0
votes
0
replies
1.7k
views
Batch effect and CCA
CCA
RNA-Seq
seurat
batch-effect
updated 1 day ago by
Ram
43k • written 5.1 years ago by
akivab2
▴ 110
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq
RNA-Seq
batch-effect
DESeq2
updated 1 day ago by
Ram
43k • written 5.1 years ago by
grant.hovhannisyan
★ 2.6k
1
vote
0
replies
663
views
Conditions for valid batch effect correction
r
batch-effect
updated 2 days ago by
Ram
43k • written 5.1 years ago by
Sebastian Hesse
▴ 340
0
votes
3
replies
1.8k
views
How to remove batch effect in copy number segment mean
Combat
CNA
Batch-Effect
updated 1 day ago by
Ram
43k • written 5.5 years ago by
sugus
▴ 150
0
votes
0
replies
1.7k
views
Differential expression using Scran batch corrected data
single-cell
Batch-effect
RNA-Seq
Scran
updated 13 hours ago by
Ram
43k • written 5.4 years ago by
baldissera152
▴ 10
1
vote
3
replies
6.1k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID
org.Dr.eg.db
updated 2 days ago by
Ram
43k • written 5.5 years ago by
modarzi
▴ 170
0
votes
0
replies
834
views
Estimating sequence complexity of DNA sequence from fasta file
sequence
RepeatMasker
pacbio
updated 2 days ago by
Ram
43k • written 5.6 years ago by
epaminonda
▴ 10
0
votes
0
replies
1.3k
views
which value from ruvadj in missMethyl can present methylation status
R
RUV
methylation
missmethyl
batch-effect
updated 2 days ago by
Ram
43k • written 5.9 years ago by
RC
▴ 20
0
votes
1
reply
1.3k
views
About BatchQC packages error
Batch-effect
R
updated 1 day ago by
Ram
43k • written 6.0 years ago by
Jun
• 0
0
votes
0
replies
1.5k
views
RIPSeeker viewRIP function fails to extract values() in GRangesList/S4 object
RIPSeq
S4
RIP
R
updated 2 days ago by
Ram
43k • written 6.2 years ago by
CrisMar
▴ 80
0
votes
1
reply
2.8k
views
Can't make sva comparison despite very distinct batch effects
sva
batch-effect
updated 1 day ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
0
votes
0
replies
1.1k
views
Finding wobble/redundant positions in an RNA string using R.
RNA
wobble-position
R
updated 2 days ago by
Ram
43k • written 6.2 years ago by
fawazfebin
▴ 100
1
vote
1
reply
2.7k
views
Plotting a PCA Plot from SVASeq results
pca
ruvseq
sva
svaseq
batch-effect
updated 2 days ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
0
votes
0
replies
1.8k
views
How to get Gene Co-expression Network from RNA seq data using cor() function?
RNA-Seq
gene-expression-matrix
correlation
R
updated 2 days ago by
Ram
43k • written 6.3 years ago by
aiswaryabioinfo
▴ 30
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS
exome-sequencing
batch-effect
updated 13 hours ago by
Ram
43k • written 6.5 years ago by
Alternative
▴ 270
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch-effect
updated 2 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
0
votes
1
reply
1.8k
views
Advice required for remove batch effect which perfectly collinear with contrast of interest
RNA-seq
batch-effect
updated 13 hours ago by
Ram
43k • written 6.6 years ago by
boymin2020
▴ 80
0
votes
0
replies
2.6k
views
Removing batch effects from methylation beta values for molecular subtyping/cluster analysis
clustering
beta-values
batch-effect
methylation
updated 2 days ago by
Ram
43k • written 6.7 years ago by
alecmchiu
• 0
0
votes
1
reply
1.2k
views
Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
random-effects
RNA-Seq
batch-effect
updated 2 days ago by
Ram
43k • written 6.7 years ago by
Dipro
• 0
1
vote
1
reply
1.7k
views
sea corrected expression matrix
sva
microarrays
batch-effect
updated 2 days ago by
Ram
43k • written 6.8 years ago by
ATCG
▴ 380
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 13 hours ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
0
votes
0
replies
2.0k
views
NOISeq Batch Correction to RNA-seq data
Batch-effect
RNA-Seq
ARSyNseq
limma
NOISeq
updated 13 hours ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
3
votes
4
replies
3.4k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 13 hours ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 13 hours ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
0
votes
0
replies
1.9k
views
Correcting batch effect from known variables in RnBeads using Combat
Combat
450k
methylation
RnBeads
batch-effect
updated 13 hours ago by
Ram
43k • written 7.1 years ago by
rahel14350
▴ 40
1
vote
0
replies
1.8k
views
Using SVA with RRBS data
sva
batch-effect
RRBS
updated 2 days ago by
Ram
43k • written 7.1 years ago by
mrodrigues.fernanda
▴ 50
0
votes
0
replies
1.5k
views
minifi for RRBS
rrbs
batch-effect
methylation
updated 2 days ago by
Ram
43k • written 7.1 years ago by
German.M.Demidov
★ 2.9k
158 results • Page
3 of 4
Recent Votes
How to compare the quality of assemblies
Filtration Of Reads With Length Lower Than 30 From Bam
Answer: Filtration Of Reads With Length Lower Than 30 From Bam
Answer: How to compare the quality of assemblies
Comment: How to compare the quality of assemblies
Bedtools merge but only if intersection exists
Answer: Korean reference file
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Answer: Prediction of Ribosomal RNA Genes Using RNAmmer Software
by
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6.3k
Another alternative is the truly free implementation barrnap https://github.com/tseemann/barrnap. This is also installable via conda so qui…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
by
Hagen
• 0
thanks! This saved me quite some time, I was about to write code to calculate the aligned length from the CIGAR.
Comment: Per base sequence content failed miserably
by
Kai Xin
• 0
will look into that. Thank you very much
Comment: Korean human genome reference file
by
SeoGyun
• 0
Thanks..... But I want to do imputation, so I have to make it as a vcf file, but the site only has a fatsa file....
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thank you for your reply https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md i saw this github tutorial for miRNA quantifica…
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Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
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▴ 500
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
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by
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14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Answer: Adding CB tag to bam file
by
swbarnes2
14k
Shouldn't you use PicardTools for this?
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
Sure. Or, one could do: bash try.bash "Homo sapiens" AHR | xargs -I v_pdb curl -s -o v_pdb.pdb https://files.rcsb.org/view/v_pdb.pdb
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
thank you so much
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
This may be the best option. Get the PDB ID's $ ./get.sh "Mus musculus" AHR 4M4X 5NJ8 5V0L 8H77 Then use `curl` to g…
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
It gives you the first 25 results though. I'll see if I can change that. EDIT: I've updated that number to 250. I'm hoping you won't need …
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
thank you very much
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