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95 results • Page
2 of 2
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1
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Tool:
DASC -- detecting hidden batch effects in gene expression datasets (Array/RNA-Seq/scRNA-Seq)
RNA-Seq
scRNA-Seq
R
Batch-Effect
updated 30 minutes ago by
Ram
43k • written 6.8 years ago by
Ar
★ 1.1k
1
vote
3
replies
3.3k
views
How to correct for batch effect in microarray meta-analysis
ComBat
microarray
meta-analysis
batch-effect
updated 32 minutes ago by
Ram
43k • written 9.9 years ago by
BrunoGiotti
▴ 120
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 30 minutes ago by
Ram
43k • written 4.5 years ago by
Lucy
▴ 140
1
vote
4
replies
1.7k
views
Batch correction and DE analysis of miRNA Seq data
miRNAseq
Differential-Expression
batch-effect
updated 28 minutes ago by
Ram
43k • written 5.0 years ago by
georgians
▴ 50
1
vote
4
replies
13k
views
RNA sequencing data batch effect removal
RNA-Seq
batch-effect
updated 27 minutes ago by
Ram
43k • written 7.4 years ago by
Tenghui Chen
• 0
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 20 minutes ago by
Ram
43k • written 7.6 years ago by
Lluís R.
★ 1.2k
0
votes
0
replies
39
views
traying to make a maf from an already annotated vcf
vcf2maf
VEP
maftools
updated 3 hours ago by
Ram
43k • written 3 hours ago by
Javier
• 0
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 38 minutes ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
0
votes
0
replies
37
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
3 hours ago by
enferdeflame
• 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 30 minutes ago by
Ram
43k • written 7.1 years ago by
rahel14350
▴ 40
0
votes
0
replies
65
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 4 hours ago by
Ram
43k • written 10 hours ago by
bioinfo223
▴ 10
0
votes
0
replies
1.9k
views
batch effect in radseq
radseq
batch-effect
SNP
updated 36 minutes ago by
Ram
43k • written 7.4 years ago by
oselm
▴ 50
0
votes
0
replies
58
views
News:
Course - Agent-Based Modelling Using NetLogo - University of Lodz, Poland
Netlogo
Individual-Based-Models
Agent-Based-Models
updated 4 hours ago by
Ram
43k • written 7 hours ago by
carlopecoraro2
★ 2.5k
0
votes
3
replies
272
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
updated 20 minutes ago by
GenoMax
141k • written 1 day ago by
Kai Xin
• 0
0
votes
4
replies
1.2k
views
Batch effects
Batch-effect
transcriptomics
updated 35 minutes ago by
Ram
43k • written 2.6 years ago by
BioQueen
▴ 30
0
votes
2
replies
268
views
How can I solve this error?
metal
15 hours ago by
22211020193
• 0
0
votes
0
replies
55
views
News:
Online course: Meta-analysis in R
Meta-Analysis
Statistics
R
updated 4 hours ago by
Ram
43k • written 5 hours ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
186
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 4 hours ago by
Ram
43k • written 10 hours ago by
rrehimi
• 0
0
votes
1
reply
143
views
DEseq2
RNA-seq
DESeq2
updated 4 hours ago by
Ram
43k • written 9 hours ago by
rrehimi
• 0
0
votes
1
reply
2.8k
views
Can't make sva comparison despite very distinct batch effects
sva
batch-effect
updated 22 hours ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
0
votes
1
reply
352
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 4 hours ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
0
votes
0
replies
712
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq
scRNA-Seq
batch-effect
updated 24 minutes ago by
Ram
43k • written 3.4 years ago by
hkarakurt
▴ 180
0
votes
1
reply
135
views
10x VDJ (TCR/BCR) BAM to fastq
TCR
VDJ
BCR
10x
updated 6 hours ago by
GenoMax
141k • written 8 hours ago by
predeus
★ 1.9k
0
votes
1
reply
790
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR
Batch-effect
RNA-Seq
updated 30 minutes ago by
Ram
43k • written 3.7 years ago by
jordan15
• 0
0
votes
2
replies
295
views
How to add motifs in cellranger-arc reference?
gtf
scRNAseq
fasta
cellranger
updated 6 hours ago by
Ehsan
• 0 • written 8 weeks ago by
bioinfo
▴ 150
0
votes
7
replies
1.8k
views
Batch effect correction in RNASeq data and plot Dendrograms cluster
clustering
dendrogram
RNA-Seq
batch-effect
updated 30 minutes ago by
Ram
43k • written 4.0 years ago by
Ankit
▴ 500
0
votes
0
replies
59
views
Tutorial:
DNA Methylation: Sequencing Techniques
WGBS
RRBS
8 hours ago by
Novogene
▴ 410
0
votes
0
replies
1.2k
views
Batch estimate using kBET
batch-effect
kbet
updated 29 minutes ago by
Ram
43k • written 4.0 years ago by
getanid123
• 0
0
votes
0
replies
111
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
17 hours ago by
renan.igor
• 0
0
votes
2
replies
255
views
GSEA analysis in R
GSEA
R
Arabidopsis
10 hours ago by
Sudip
• 0
0
votes
0
replies
73
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
10 hours ago by
P.
• 0
0
votes
4
replies
386
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
12 hours ago by
feather-W
• 0
0
votes
0
replies
78
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
13 hours ago by
ekirsch
• 0
0
votes
0
replies
97
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
19 hours ago by
synat.keam
▴ 100
0
votes
3
replies
3.0k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 28 minutes ago by
Ram
43k • written 8.9 years ago by
siddharth.patel.153
• 0
0
votes
2
replies
1.2k
views
Normalization (microarray data)
microarray
Normalization
Batch-effect
updated 40 minutes ago by
Ram
43k • written 6.3 years ago by
j_jamal96
▴ 20
0
votes
0
replies
44
views
Difference when using difference number of pathways score to compare between 3 groups
Limma
GSVA
1 hour ago by
Chris
▴ 260
0
votes
0
replies
1.7k
views
Differential expression using Scran batch corrected data
single-cell
Batch-effect
RNA-Seq
Scran
updated 20 minutes ago by
Ram
43k • written 5.4 years ago by
baldissera152
▴ 10
0
votes
1
reply
2.9k
views
Microarray batch effect correction
Microarray
Batch-effect
updated 35 minutes ago by
Ram
43k • written 6.6 years ago by
sarahmanderni
▴ 100
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 39 minutes ago by
Ram
43k • written 6.6 years ago by
boymin2020
▴ 80
0
votes
0
replies
37
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 2 hours ago by
Ram
43k • written 2 hours ago by
samuelkalandarov2002
• 0
0
votes
3
replies
3.2k
views
Batch correction (mass spectrometry data)
Combat
R
SVA
Biostatistics
batch-effect
updated 20 minutes ago by
Ram
43k • written 7.4 years ago by
mkhadka10
• 0
0
votes
1
reply
84
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
updated 3 hours ago by
Ram
43k • written 3 hours ago by
_quantum_girl_
▴ 10
0
votes
0
replies
2.0k
views
NOISeq Batch Correction to RNA-seq data
Batch-effect
RNA-Seq
ARSyNseq
limma
NOISeq
updated 40 minutes ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
0
votes
1
reply
186
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 21 hours ago by
GenoMax
141k • written 21 hours ago by
ycts
• 0
95 results • Page
2 of 2
Recent Votes
A: Out Of Disk Space With Picard Tools ?
Exporting WGCNA step-to-step network construction objects into igraph object
Comment: Downloaded pdb's on rcsb.org
Answer: How to compare the quality of assemblies
How to compare the quality of assemblies
A: Best strategy for gene annotation for de novo genome assembly without RNA-seq da
Comment: Questions about a bug when transferring cram file to bam file
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Recent Awards •
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Commentator
to
GenoMax
141k
Centurion
to
jkbonfield
★ 1.2k
Popular Question
to
yueli7
▴ 250
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Randy H
▴ 110
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lefthandgergo
▴ 10
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Juke34
8.5k
Recent Replies
Comment: Per base sequence content failed miserably
by
GenoMax
141k
If this is 16S sequencing just follow the standard workflows like Qiime2.https://docs.qiime2.org/2024.2/tutorials/overview/
Comment: Out Of Disk Space With Picard Tools ?
by
kjngo
• 0
Thanks changing the tmp dir fixed the out of disk space error for me as well.
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
Download services for PDB are described on this page: https://www.rcsb.org/docs/programmatic-access/file-download-services It could be as …
Answer: How to compare the quality of assemblies
by
shelkmike
★ 1.2k
Since BUSCO results are almost identical but the assembly sizes differ significantly, I suppose that the difference between the assemblies …
Comment: differential gene expression analysis when not all samples have an untreated cou
by
nhaus
▴ 300
Thank you very much for your answer, that was very helpful! > Impossible to say. It depends on your data, particularly on how the donors …
Comment: QC exclusion of A/T or G/C alleles to avoid strand issues
by
bk11
★ 2.3k
This could be because they are probably merging two or more datasets. If you are merging two or more datasets, it will be very important th…
Answer: Problem with Mirdeep2 and Randfold output
by
otieno43
▴ 30
I sorted this out by first removing white space in the first line of the reference genome. Then indexed, the ran the mapper.pl script follo…
Comment: Questions about a bug when transferring cram file to bam file
by
GenoMax
141k
Just to be certain, you are saying that if OP runs `samtools view` without the explicit reference it will be automatically downloaded from …
Comment: Questions about a bug when transferring cram file to bam file
by
jkbonfield
★ 1.2k
That SQ M5 is chr1 in my copy of GRCh38 (Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa). I'm assuming your hg38.fa is not the sa…
Comment: What happened to Tombo Re-squiggle
by
Ram
43k
Please do not add answers unless you're answering the top level question. Instead, use `Add Comment` or `Add Reply` as appropriate. I've mo…
Comment: What happened to Tombo Re-squiggle
by
Joseph
• 0
Hi, Does anybody has the answer to this? I also want to resquiggle my data with Remora but do not quite get which is the appropriate com…
Comment: How To Identify The 16S Rrna Gene Sequence In A Genome
by
colindaven
6.3k
It's also worth mentioning `Barrnap` is in the bacterial annotation system **Prokka**. `Prokka` can be installed on Debian systems with `…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
Elisabeth Gasteiger
★ 2.4k
See also https://www.uniprot.org/help/negative_datasets
Comment: Sheep reference genome remapping coordinates
by
valentinatsar
• 0
Thank you for your response As I can understand this tool takes sequence input files right? I have genome-wide genotypes instead of sequen…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
me
▴ 750
Ok I made this into an answer. Could you please accept it as such.
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