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362 results • Page
4 of 8
Sort: Views
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Views
Votes
Replies
1
vote
1
reply
1.3k
views
Can we use previous estimated ComBat model to correct batch effects for new data?
microarray
RNA-Seq
batch-effect
updated 1 day ago by
Ram
43k • written 5.0 years ago by
Min Dai
▴ 160
15
votes
6
replies
1.2k
views
6 follow
VCF to human friendly form?
vcf
visualization
updated 4 days ago by
Pierre Lindenbaum
161k • written 19 months ago by
wormball
▴ 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
0
votes
2
replies
1.2k
views
Normalization (microarray data)
microarray
Normalization
Batch-effect
updated 16 hours ago by
Ram
43k • written 6.3 years ago by
j_jamal96
▴ 20
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
0
votes
4
replies
1.2k
views
Batch effects
Batch-effect
transcriptomics
updated 15 hours ago by
Ram
43k • written 2.6 years ago by
BioQueen
▴ 30
7
votes
3
replies
1.2k
views
biomaRt::getSequence - Invalid type argument
biomaRt
R
updated 2 days ago by
Ram
43k • written 3.8 years ago by
mbk0asis
▴ 680
8
votes
5
replies
1.2k
views
Classifying repeat features from Ensembl
ensembl
repeat
updated 3 days ago by
e.r.zakiev
▴ 190 • written 15 months ago by
liorglic
★ 1.4k
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
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 15 hours ago by
Ram
43k • written 4.0 years ago by
getanid123
• 0
1
vote
9
replies
1.1k
views
Supergnova stuck in tutorial
Genetic
Correlations
Python
Supergnova
Conda
updated 23 hours ago by
Murat
• 0 • written 19 months ago by
Gerard
▴ 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
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
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
2
votes
2
replies
1.1k
views
Can we directly use batch corrected gene expression (Bulk RNA-seq) for further downstream analyses?
RNA-Seq
batch-effect
updated 15 hours ago by
Ram
43k • written 5.0 years ago by
tigeradab
▴ 60
0
votes
3
replies
1.1k
views
Discrepancy between E() Values in Blastp Search - HELP
BLAST
E-value
Blastp
Protein
updated 1 day ago by
Ram
43k • written 5.3 years ago by
minasmayth
• 0
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
0
votes
16
replies
1.0k
views
What is the sequence origin in human plasma?
human
sequence
cfDNA
6 days ago by
biwdpang
• 0
5
votes
2
replies
1.0k
views
How to perform batch correction when we have only single condition?
sva
combat
batch-effect
DESeq2
updated 2 days ago by
Ram
43k • written 3.7 years ago by
svp
▴ 680
1
vote
3
replies
1.0k
views
problem with facing strange gene name in TCGA data
TCGA
RNA-Seq
batch-effect
updated 2 days ago by
Ram
43k • written 5.6 years ago by
modarzi
▴ 170
3
votes
2
replies
1.0k
views
Can I take 'organ type' as a batch effect and use ComBat to remove organ dependent variations?
RNA-Seq
Cross-Species
SVA
ComBat
Batch-Effect
updated 2 days ago by
Ram
43k • written 4.6 years ago by
rodguinea
• 0
7
votes
7
replies
1.0k
views
Prediction tools summary - zero values
statistics
updated 2 days ago by
Дана
• 0 • written 6 months ago by
Lukas
▴ 50
3
votes
7
replies
1.0k
views
Can I use batch effect correction "by parts"?
ComBat
RNA-Seq
batch-effect
updated 1 day ago by
Ram
43k • written 4.3 years ago by
n,n
▴ 360
2
votes
2
replies
1.0k
views
Batch correct batch 2 while leaving batch 1 unchanged.
limma
machine-learning
batch-effect
updated 15 hours ago by
Ram
43k • written 3.7 years ago by
i.sudbery
19k
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
2
votes
5
replies
985
views
Ties in reranked list
fgsea
GSEA
updated 5 days ago by
Gordon
• 0 • written 6 months ago by
Hamza
• 0
2
votes
3
replies
965
views
Treating "patient" as a batch effect
ComBat_seq
DESeq2
batch-Effect
updated 2 days ago by
Ram
43k • written 17 months ago by
Mia
▴ 20
2
votes
2
replies
944
views
Is there a file information dictionary for files downloaded from ENCODE through batch download?
ENCODE
updated 2 days ago by
Ram
43k • written 4.6 years ago by
burcakotlu
▴ 40
2
votes
3
replies
926
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
2
votes
2
replies
885
views
Method to detect genome doubling
CNV
genome doubling
updated 1 day ago by
Zhenyu Zhang
★ 1.2k • written 4.5 years ago by
CY
▴ 750
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
3
votes
6
replies
879
views
Any problem re-using last year's RNA-Seq data in this year's analysis?
RNA-Seq
batch-effect
updated 2 days ago by
Ram
43k • written 3.7 years ago by
oakhamwolf
▴ 20
2
votes
6
replies
848
views
Batch effect correction with cell type enrichment analysis
limma
RNA-seq
r
batch-effect
updated 2 days ago by
Ram
43k • written 18 months ago by
JACKY
▴ 140
5
votes
5
replies
835
views
Blacklist for bacterial genome [ChIPseq]?
ChIPseq
Blacklist
updated 6 days ago by
Ram
43k • written 10 months ago by
Emily Wasson
▴ 30
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
7
votes
7
replies
833
views
Forum:
Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
Career
advice
updated 3 days ago by
Dunois
★ 2.5k • written 4 days ago by
AdviceSeeker
• 0
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
3
replies
817
views
add INFO tag to vcf with bcftools
bcftools
vcf
updated 2 days ago by
Ram
43k • written 23 months ago by
from the mountains
▴ 230
0
votes
2
replies
810
views
Is it correct to merge two raw CEL datasets and then perform quality control, background correction, and normalization on it?
R
microarray
affymetrix
batch-effect
quality-control
updated 2 days ago by
Ram
43k • written 2.8 years ago by
Sib
▴ 60
0
votes
1
reply
804
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR
Batch-effect
RNA-Seq
updated 15 hours ago by
Ram
43k • written 3.7 years ago by
jordan15
• 0
3
votes
2
replies
802
views
Retrieve initial query in getBM()
getBM
biomaRt
R
gene
updated 2 days ago by
Ram
43k • written 3.1 years ago by
helia.ziaei
• 0
1
vote
2
replies
802
views
What type of normalization does removeBatchEffect function require as the input?
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 2 days ago by
Ram
43k • written 20 months ago by
ev97
▴ 20
4
votes
13
replies
766
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 2 days ago by
BioinfGuru
★ 1.7k • written 7 days ago by
matteo.levorato
• 0
0
votes
0
replies
727
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
723
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq
scRNA-Seq
batch-effect
updated 15 hours ago by
Ram
43k • written 3.4 years ago by
hkarakurt
▴ 180
11
votes
12
replies
692
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 11 hours ago by
Ram
43k • written 17 hours ago by
iamsmor
• 0
2
votes
7
replies
682
views
Removing duplicates
duplicates
ONT
minimap2
updated 11 hours ago by
joe
▴ 500 • written 1 day ago by
quentinperriere
• 0
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
8
votes
10
replies
658
views
bash script
whole-genome-sequencing
updated 3 days ago by
Ram
43k • written 11 days ago by
bestone
▴ 30
362 results • Page
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it worked. Thank you. Now my terminal is crashing, seems 16gb of RAM and 4 cores isn't enough. Can you suggest something?
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I checked Picard ```AddOrReplaceReadsGroups``` and ```AddOATag```. Is that what you're referring to?
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will look into that. Thank you very much
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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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No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
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Shouldn't you use PicardTools for this?
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