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96 results • Page
1 of 2
Sort: replies
Rank
Views
Votes
Replies
22
votes
18
replies
6.1k
views
about batch correction in scRNA-seq
scRNA
scRNA-seq
batch-effect
updated 13 hours ago by
Ram
43k • written 4.5 years ago by
Bogdan
★ 1.4k
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read
length
bam
updated 10 minutes ago by
Hagen
▴ 10 • written 10.2 years ago by
filipzembol
▴ 180
11
votes
12
replies
656
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 9 hours ago by
Ram
43k • written 15 hours ago by
iamsmor
• 0
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 13 hours ago by
kjngo
• 0 • written 12.0 years ago by
Gabriel R.
★ 2.9k
2
votes
10
replies
590
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 16 hours ago by
GenoMax
141k • written 1 day ago by
me
• 0
9
votes
10
replies
6.8k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat
scRNA-seq
Harmony
RNA-seq
batch-effect
updated 13 hours ago by
Ram
43k • written 4.5 years ago by
Lucy
▴ 140
1
vote
9
replies
1.1k
views
Supergnova stuck in tutorial
Genetic
Correlations
Python
Supergnova
Conda
updated 21 hours ago by
Murat
• 0 • written 19 months ago by
Gerard
▴ 10
1
vote
9
replies
619
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 18 hours ago by
Elisabeth Gasteiger
★ 2.4k • written 23 hours ago by
Jacky
• 0
3
votes
8
replies
4.1k
views
Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
fpkm
scRNA-seq
RNA-Seq
tpm
batch-effect
updated 13 hours ago by
Ram
43k • written 4.5 years ago by
hkarakurt
▴ 180
3
votes
8
replies
4.9k
views
An idea to identify batch effects
microarray
batch-effect
updated 13 hours ago by
Ram
43k • written 9.6 years ago by
mjarosz
• 0
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
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat
RNA-Seq
Limma
DESeq2
batch-effect
updated 13 hours ago by
Ram
43k • written 4.9 years ago by
borkk
▴ 140
0
votes
7
replies
1.8k
views
Batch effect correction in RNASeq data and plot Dendrograms cluster
clustering
dendrogram
RNA-Seq
batch-effect
updated 13 hours ago by
Ram
43k • written 4.0 years ago by
Ankit
▴ 500
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 17 hours ago by
colindaven
6.3k • written 10.9 years ago by
Ontheway
▴ 10
2
votes
6
replies
5.1k
views
How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq?
scRNA-seq
R
seurat
harmony
batch-effect
updated 13 hours ago by
Ram
43k • written 3.7 years ago by
Lukadon77
• 0
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
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
4
replies
396
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
1 hour ago by
Kai Xin
• 0
3
votes
4
replies
344
views
biomaRt error for different R version
biomaRt
R
updated 19 hours ago by
GenoMax
141k • written 1 day ago by
manaswwm
▴ 490
1
vote
4
replies
366
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
updated 19 hours ago by
GenoMax
141k • written 23 hours ago by
n_navy
• 0
5
votes
4
replies
516
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq
EdgeR
DEGs
DESeq2
12 hours ago by
BioinfGuru
★ 1.7k
2
votes
4
replies
6.0k
views
Batch Effect Removal in RNA-Seq Data for DGE & WGCNA. Should I omit any samples according to PCA plots?
Batch-effect
RNA-Seq
R
DESeq2
updated 13 hours ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
1
vote
4
replies
13k
views
RNA sequencing data batch effect removal
RNA-Seq
batch-effect
updated 13 hours ago by
Ram
43k • written 7.4 years ago by
Tenghui Chen
• 0
1
vote
4
replies
1.7k
views
Batch correction and DE analysis of miRNA Seq data
miRNAseq
Differential-Expression
batch-effect
updated 13 hours ago by
Ram
43k • written 5.0 years ago by
georgians
▴ 50
1
vote
4
replies
582
views
What happened to Tombo Re-squiggle
Tombo
resquiggle
ONT
updated 16 hours ago by
Ram
43k • written 3 months ago by
turcoa1
• 0
0
votes
4
replies
1.2k
views
Batch effects
Batch-effect
transcriptomics
updated 13 hours ago by
Ram
43k • written 2.6 years ago by
BioQueen
▴ 30
1
vote
4
replies
1.4k
views
Removing/Accounting for batch effects in unbalanced group RNAseq data
rna-seq
batch-effect
deseq
updated 13 hours ago by
Ram
43k • written 2.2 years ago by
claysandel
• 0
1
vote
4
replies
3.1k
views
remove batch effect for multiple tumor data
RNA-Seq
batch-effect
updated 13 hours ago by
Ram
43k • written 7.1 years ago by
hellocita
▴ 40
1
vote
3
replies
2.0k
views
gene expression data analysis and batch effect methods
microarray
Gene-expression
batch-effect
updated 13 hours ago by
Ram
43k • written 6.9 years ago by
Shamim Sarhadi
▴ 220
2
votes
3
replies
349
views
Sheep reference genome remapping coordinates
reference
remap
sheep
coordinates
genome
19 hours ago by
valentinatsar
• 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
9
votes
3
replies
6.9k
views
EdgeR-GLMs correcting for batch effects
RNA-Seq
edgeR
Batch-Effect
updated 13 hours ago by
Ram
43k • written 9.9 years ago by
Matina
▴ 250
1
vote
3
replies
3.3k
views
How to correct for batch effect in microarray meta-analysis
ComBat
microarray
meta-analysis
batch-effect
updated 13 hours ago by
Ram
43k • written 9.9 years ago by
BrunoGiotti
▴ 120
2
votes
3
replies
1.5k
views
RNASeq - How to compare the expression of a single gene across batches
RNA-Seq
edgeR
batch-effect
updated 13 hours ago by
Ram
43k • written 3.5 years ago by
oakhamwolf
▴ 20
1
vote
3
replies
3.6k
views
Does Harmony batch correction for scRNA-seq require the same populations to be present in all samples?
Harmony
single-cell
scRNA-seq
batch-effect
updated 13 hours ago by
Ram
43k • written 4.5 years ago by
Lucy
▴ 140
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
0
votes
3
replies
3.2k
views
Batch correction (mass spectrometry data)
Combat
R
SVA
Biostatistics
batch-effect
updated 13 hours ago by
Ram
43k • written 7.4 years ago by
mkhadka10
• 0
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
3
replies
3.0k
views
Quick way to Identify batch effect from covariates?
bioconductor
batch-effect
updated 13 hours ago by
Ram
43k • written 7.9 years ago by
James Ashmore
★ 3.4k
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
3
votes
3
replies
324
views
Korean human genome reference file
GWAS
reference
imputation
3 hours ago by
SeoGyun
• 0
7
votes
3
replies
2.5k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 40 minutes ago by
colindaven
6.3k • written 15 months ago by
Dr.Animo
▴ 130
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 13 hours ago by
Ram
43k • written 5.0 years ago by
tigeradab
▴ 60
0
votes
2
replies
511
views
autodockvina
python
python3
autodock
updated 11 hours ago by
Ram
43k • written 3 months ago by
iamsmor
• 0
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 13 hours ago by
Ram
43k • written 9.1 years ago by
chengzhao41
▴ 110
4
votes
2
replies
251
views
Assume "yes" as the answer to any prompts with bioconda
docker
container
bioconda
updated 20 hours ago by
Juke34
8.5k • written 21 hours ago by
njornet
▴ 20
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
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
3
votes
2
replies
4.1k
views
Batch effects in sequencing data
batch-effect
updated 13 hours ago by
Ram
43k • written 8.7 years ago by
Andrew
▴ 60
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
96 results • Page
1 of 2
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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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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