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33 results • Page
1 of 1
Sort: Views
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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 21 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 21 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 21 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 21 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 21 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 21 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 21 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 21 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 21 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 21 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 21 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 21 hours ago by
Ram
43k • written 18 months ago by
Dominique
• 0
0
votes
0
replies
1.2k
views
Batch estimate using kBET
batch-effect
kbet
updated 21 hours ago by
Ram
43k • written 4.0 years ago by
getanid123
• 0
0
votes
1
reply
808
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR
Batch-effect
RNA-Seq
updated 21 hours ago by
Ram
43k • written 3.7 years ago by
jordan15
• 0
0
votes
0
replies
727
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq
scRNA-Seq
batch-effect
updated 21 hours ago by
Ram
43k • written 3.4 years ago by
hkarakurt
▴ 180
2
votes
7
replies
707
views
Removing duplicates
duplicates
ONT
minimap2
updated 16 hours ago by
joe
▴ 510 • written 2 days ago by
quentinperriere
• 0
0
votes
2
replies
517
views
autodockvina
python
python3
autodock
updated 19 hours ago by
Ram
43k • written 3 months ago by
iamsmor
• 0
0
votes
4
replies
478
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
9 hours ago by
Kai Xin
• 0
0
votes
2
replies
376
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
15 hours ago by
航太郎
• 0
0
votes
1
reply
272
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
updated 15 hours ago by
cmdcolin
★ 3.8k • written 1 day ago by
renan.igor
• 0
0
votes
2
replies
255
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
10 hours ago by
Ashok
• 0
0
votes
2
replies
240
views
python file for coding potential calculator
cpc2.py
12 hours ago by
Ashok
• 0
0
votes
2
replies
235
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
12 hours ago by
Ashok
• 0
3
votes
2
replies
199
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
1 hour ago by
joe
▴ 510
0
votes
2
replies
196
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
30 minutes ago by
_quantum_girl_
▴ 10
0
votes
0
replies
112
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
20 hours ago by
Chris
▴ 260
0
votes
0
replies
96
views
create genewise sync file in popoolation
popoolation
updated 19 hours ago by
GenoMax
141k • written 20 hours ago by
N.Y.Wiyana-Hewage
• 0
0
votes
0
replies
74
views
Lncipedia GTF file error
Proteomics
updated 23 minutes ago by
Ram
43k • written 8 hours ago by
atharvakarkare14
▴ 10
0
votes
1
reply
62
views
Could you please assist in identifying this cluster?
single-cell
updated 27 minutes ago by
Ram
43k • written 1 hour ago by
Kazo
• 0
0
votes
0
replies
60
views
miRDeep2: How to get the read counts
mirdeep2
6 hours ago by
Atul K.
• 0
0
votes
0
replies
54
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 20 minutes ago by
Ram
43k • written 4 hours ago by
Dinmukhamed
• 0
0
votes
0
replies
21
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
1 hour ago by
DanielEB_fisk
▴ 20
0
votes
0
replies
20
views
Copy number variation plot
Copy-number-variation
genomics
updated 12 minutes ago by
Ram
43k • written 27 minutes ago by
Emmi
• 0
33 results • Page
1 of 1
Recent Votes
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Comment: Illumina reads preprocessing best practice for snp calling applications
Installing/switching between versions of R/Rstudio/Bioconductor
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Recent Replies
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
by
Ram
43k
Your tutorial required `sudo` and thus is not doable for a majority of people. Any alternative to `sudo snap`?
Comment: Should I apply doublet detection for each pool seperately?
by
Ram
43k
Do not delete posts that have received feedback,
Comment: QC exclusion of A/T or G/C alleles to avoid strand issues
by
_quantum_girl_
▴ 10
They aren't merging any datasets. Just for reference the paper is this: https://www.nature.com/articles/s41380-022-01674-9#MOESM1. Citing: …
Comment: RNA seq differential expression analysis
by
BioinfGuru
★ 1.7k
https://help.galaxyproject.org/
Answer: RNA seq differential expression analysis
by
Mohamed Abderrahmane
▴ 10
The tool RSEM, which performs transcript quantification for RNA-Seq data, provides FPKM.
Comment: Illumina reads preprocessing best practice for snp calling applications
by
Enrique
• 0
Hi! I'm still interested in the step that you use for the SNP calling. Did you use `trimmomatic` or another tool for trimming before mappin…
Comment: Could you please assist in identifying this cluster?
by
ATpoint
81k
The information do not suffice. Please show plots and identified marker genes. Also, make sure it is not a trash cluster with low number of…
Comment: Free/open source 23andme-like analysis
by
joe
▴ 510
Thank you, I added 'accurate' now ;) I'm surprised to find out that there isn't some tool like multiqc that just summarizes all this infor…
Comment: Memory usage of picard Samsort
by
ATpoint
81k
Guys, just use `samtools sort` which won't get you into trouble with any of that.
Comment: Ciriquant not configuring hisat2 indexed files
by
Carlo Yague
8.6k
I don't know for sure, but I think that decreasing the amount of threads (1 or 2 instead of 4) will decrease the memory requirements of the…
Answer: Memory usage of picard Samsort
by
tamas.malkocs
• 0
For me, setting `TMP_DIR` (`--TMP_DIR /home/tmp`) didn't work in picard 2.21.1. What solved the issue was setting the environmental variabl…
Answer: Plink merge errors.
by
Dinmukhamed
• 0
I found answer https://www.biostars.org/p/101191/.
Comment: Ciriquant not configuring hisat2 indexed files
by
Atul K.
• 0
it worked. Thank you. Now my terminal is crashing, seems 16gb of RAM and 4 cores isn't enough. Can you suggest something?
Comment: Adding CB tag to bam file
by
Maria
• 0
I checked Picard ```AddOrReplaceReadsGroups``` and ```AddOATag```. Is that what you're referring to?
Comment: Free/open source 23andme-like analysis
by
Michael
54k
Noted that 'accurate' wasn't among your criteria ;) Anyway, most variant callers are free open-source software. However, for ancestry ana…
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