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37 results • Page
1 of 1
Sort: Views
Rank
Views
Votes
Replies
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 13 hours ago by
Ram
43k • written 7.6 years ago by
Lluís R.
★ 1.2k
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
3
replies
3.0k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 13 hours ago by
Ram
43k • written 8.9 years ago by
siddharth.patel.153
• 0
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
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
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
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
0
votes
0
replies
1.9k
views
batch effect in radseq
radseq
batch-effect
SNP
updated 13 hours ago by
Ram
43k • written 7.4 years ago by
oselm
▴ 50
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
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
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
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 13 hours ago by
Ram
43k • written 17 months ago by
Dominique
• 0
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
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
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 13 hours ago by
Ram
43k • written 3.4 years ago by
hkarakurt
▴ 180
2
votes
7
replies
674
views
Removing duplicates
duplicates
ONT
minimap2
updated 8 hours ago by
joe
▴ 500 • written 1 day ago by
quentinperriere
• 0
0
votes
2
replies
511
views
autodockvina
python
python3
autodock
updated 11 hours ago by
Ram
43k • written 3 months ago by
iamsmor
• 0
0
votes
4
replies
396
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
1 hour ago by
Kai Xin
• 0
0
votes
1
reply
373
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 17 hours ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
0
votes
2
replies
331
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
7 hours ago by
航太郎
• 0
0
votes
3
replies
314
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 9 hours ago by
swbarnes2
14k • written 23 hours ago by
rrehimi
• 0
0
votes
2
replies
279
views
GSEA analysis in R
GSEA
R
Arabidopsis
23 hours ago by
Sudip
• 0
0
votes
1
reply
235
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
updated 6 hours ago by
cmdcolin
★ 3.8k • written 1 day ago by
renan.igor
• 0
0
votes
2
replies
207
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
1 hour ago by
Ashok
• 0
0
votes
2
replies
201
views
python file for coding potential calculator
cpc2.py
4 hours ago by
Ashok
• 0
0
votes
2
replies
195
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
4 hours ago by
Ashok
• 0
0
votes
1
reply
154
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
updated 16 hours ago by
Ram
43k • written 16 hours ago by
_quantum_girl_
▴ 10
0
votes
0
replies
97
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 17 hours ago by
Ram
43k • written 23 hours ago by
bioinfo223
▴ 10
0
votes
0
replies
87
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
12 hours ago by
Chris
▴ 260
0
votes
0
replies
85
views
traying to make a maf from an already annotated vcf
vcf2maf
VEP
maftools
updated 16 hours ago by
Ram
43k • written 16 hours ago by
Javier
• 0
0
votes
0
replies
83
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
10 hours ago by
rahu
• 0
0
votes
0
replies
82
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 15 hours ago by
Ram
43k • written 15 hours ago by
samuelkalandarov2002
• 0
0
votes
0
replies
80
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
17 hours ago by
enferdeflame
• 0
0
votes
0
replies
70
views
create genewise sync file in popoolation
popoolation
updated 10 hours ago by
GenoMax
141k • written 12 hours ago by
N.Y.Wiyana-Hewage
• 0
0
votes
0
replies
51
views
Free/open source 23andme-like analysis
NGS
SNPs
genomics
VCF
3 hours ago by
joe
▴ 500
0
votes
0
replies
27
views
Spam:
Free Instagram Likes
Free
Likes
Instagram
8 hours ago by
seo2
0
0
votes
0
replies
13
views
Lncipedia GTF file error
Proteomics
Bioinformatics
38 minutes ago by
atharvakarkare14
▴ 10
37 results • Page
1 of 1
Recent Votes
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
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
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Recent Replies
Answer: Prediction of Ribosomal RNA Genes Using RNAmmer Software
by
colindaven
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
▴ 10
thanks! This saved me quite some time, I was about to write code to calculate the aligned length from the CIGAR. But this can be done with …
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
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