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38 results • Page
1 of 1
Sort: Votes
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Views
Votes
Replies
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 11 hours ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray
combat
batch-effect
median-normalization
updated 11 hours ago by
Ram
43k • written 17 months ago by
Dominique
• 0
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 12 hours ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
2
votes
7
replies
668
views
Removing duplicates
duplicates
ONT
minimap2
updated 7 hours ago by
joe
▴ 500 • written 1 day ago by
quentinperriere
• 0
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 11 hours ago by
Ram
43k • written 7.6 years ago by
Lluís R.
★ 1.2k
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS
exome-sequencing
batch-effect
updated 12 hours ago by
Ram
43k • written 6.5 years ago by
Alternative
▴ 270
0
votes
0
replies
81
views
traying to make a maf from an already annotated vcf
vcf2maf
VEP
maftools
updated 15 hours ago by
Ram
43k • written 15 hours ago by
Javier
• 0
0
votes
1
reply
151
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
updated 14 hours ago by
Ram
43k • written 14 hours ago by
_quantum_girl_
▴ 10
0
votes
0
replies
76
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 14 hours ago by
Ram
43k • written 14 hours ago by
samuelkalandarov2002
• 0
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 12 hours ago by
Ram
43k • written 6.6 years ago by
boymin2020
▴ 80
0
votes
0
replies
2.0k
views
NOISeq Batch Correction to RNA-seq data
Batch-effect
RNA-Seq
ARSyNseq
limma
NOISeq
updated 11 hours ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 11 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 11 hours ago by
Ram
43k • written 7.1 years ago by
rahel14350
▴ 40
0
votes
0
replies
1.9k
views
batch effect in radseq
radseq
batch-effect
SNP
updated 11 hours ago by
Ram
43k • written 7.4 years ago by
oselm
▴ 50
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 11 hours ago by
Ram
43k • written 3.4 years ago by
hkarakurt
▴ 180
0
votes
1
reply
799
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR
Batch-effect
RNA-Seq
updated 11 hours ago by
Ram
43k • written 3.7 years ago by
jordan15
• 0
0
votes
0
replies
1.2k
views
Batch estimate using kBET
batch-effect
kbet
updated 11 hours ago by
Ram
43k • written 4.0 years ago by
getanid123
• 0
0
votes
3
replies
3.0k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 11 hours ago by
Ram
43k • written 8.9 years ago by
siddharth.patel.153
• 0
0
votes
0
replies
1.7k
views
Differential expression using Scran batch corrected data
single-cell
Batch-effect
RNA-Seq
Scran
updated 11 hours ago by
Ram
43k • written 5.4 years ago by
baldissera152
▴ 10
0
votes
0
replies
85
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
11 hours ago by
Chris
▴ 260
0
votes
2
replies
509
views
autodockvina
python
python3
autodock
updated 9 hours ago by
Ram
43k • written 3 months ago by
iamsmor
• 0
0
votes
0
replies
68
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
9 hours ago by
rahu
• 0
0
votes
0
replies
66
views
create genewise sync file in popoolation
popoolation
updated 9 hours ago by
GenoMax
141k • written 10 hours ago by
N.Y.Wiyana-Hewage
• 0
0
votes
3
replies
304
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 7 hours ago by
swbarnes2
14k • written 21 hours ago by
rrehimi
• 0
0
votes
0
replies
25
views
Spam:
Free Instagram Likes
Free
Likes
Instagram
6 hours ago by
seo2
0
0
votes
2
replies
317
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
5 hours ago by
航太郎
• 0
0
votes
1
reply
221
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
updated 5 hours ago by
cmdcolin
★ 3.8k • written 1 day ago by
renan.igor
• 0
0
votes
2
replies
189
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
2 hours ago by
Ashok
• 0
0
votes
2
replies
194
views
python file for coding potential calculator
cpc2.py
2 hours ago by
Ashok
• 0
0
votes
0
replies
30
views
Free/open source 23andme-like analysis
NGS
SNPs
genomics
VCF
2 hours ago by
joe
▴ 500
0
votes
2
replies
180
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
11 minutes ago by
Ashok
• 0
0
votes
4
replies
414
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
23 hours ago by
feather-W
• 0
0
votes
4
replies
369
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
just now by
Kai Xin
• 0
0
votes
0
replies
110
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
22 hours ago by
P.
• 0
0
votes
2
replies
277
views
GSEA analysis in R
GSEA
R
Arabidopsis
21 hours ago by
Sudip
• 0
0
votes
1
reply
372
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 15 hours ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
0
votes
0
replies
95
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 15 hours ago by
Ram
43k • written 22 hours ago by
bioinfo223
▴ 10
0
votes
0
replies
77
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
15 hours ago by
enferdeflame
• 0
38 results • Page
1 of 1
Recent Votes
Bedtools merge but only if intersection exists
Answer: Korean reference file
Comment: Korean human genome reference file
C: samtools sort bam file
A: samtools sort bam file
Answer: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
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Recent Awards •
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★ 7.0k
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yueli7
▴ 250
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141k
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Recent Replies
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....
Comment: miRNAs quantification using mirdeep2 tool
by
Ashok
• 0
thank you for your reply https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md i saw this github tutorial for miRNA quantifica…
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
by
cmdcolin
★ 3.8k
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/…
Comment: How to get the reference panel for UKBB
by
航太郎
• 0
Thanks for your guide!
Comment: Removing duplicates
by
joe
▴ 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…
Comment: RNA seq differential expression analysis
by
swbarnes2
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
Answer: Downloaded pdb's on rcsb.org
by
Ram
43k
I'm going to build off of OP's query and give them a simple script: ```bash organism=$(echo $1 | sed 's/ /%20/g') gene=$2 curl -s https:/…
Comment: miRNAs quantification using mirdeep2 tool
by
GenoMax
141k
This question does not make complete sense. If you have your own data files why do you need deep sequencing reads? Genome (can be download…
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