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1,000 results • Page
3 of 20
Sort: Views
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Views
Votes
Replies
1
vote
3
replies
3.7k
views
MSF Data Analysis
MSF
Proteomics
Thermo
Proteome Discoverer
updated 15 days ago by
iqra
• 0 • written 4.4 years ago by
JJDollar
▴ 130
5
votes
8
replies
3.6k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 10 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
2
votes
6
replies
3.6k
views
Algorithm to remove batch effects
single-cell
batch-effect
RNA-Seq
updated 2 days ago by
Ram
43k • written 3.3 years ago by
fouerghi20
▴ 80
7
votes
2
replies
3.6k
views
Timeout on getBM() to retrieve snps from locations
biomaRt
getBM
R
updated 2 days ago by
Ram
43k • written 5.2 years ago by
Corentin
▴ 600
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 23 hours ago by
Ram
43k • written 4.5 years ago by
Lucy
▴ 140
4
votes
2
replies
3.6k
views
Genome annotation: convert gtf to gff3 file
gff3
gtf
updated 25 days ago by
vague-barracuda-4686
• 0 • written 17 months ago by
shinyjj
▴ 50
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling
samtools
VCF
BCF
updated 24 days ago by
Ram
43k • written 5.5 years ago by
c.clarido
▴ 110
8
votes
12
replies
3.5k
views
Why should ATAC-seq mapped reads be shifted +4 and -5 for +strand and -strand, respectively
ATAC-seq
updated 16 days ago by
Maksim
• 0 • written 3.4 years ago by
progistar
▴ 40
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 1 day ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
1
vote
8
replies
3.4k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 2 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 2 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
7
votes
7
replies
3.4k
views
How to perform normalization when converting ATAC bam file to bigwig file using deeptools for IGV visualization
bamCoverage
deeptools
bigwig
IGV
ATAC
updated 28 days ago by
sgv
• 0 • written 2.2 years ago by
sir.outman
▴ 40
4
votes
5
replies
3.4k
views
Please clarify me about countOverlaps()?
RNA-Seq
countOverlaps
R
updated 2 days ago by
Ram
43k • written 6.3 years ago by
seta
★ 1.9k
2
votes
6
replies
3.4k
views
Base Quality of a reported variant in VCF
alignment
FASTQ
VCF
next-gen
Variant-Calling
updated 24 days ago by
Ram
43k • written 9.2 years ago by
VineethVenumadhavan
▴ 50
1
vote
3
replies
3.3k
views
How to correct for batch effect in microarray meta-analysis
ComBat
microarray
meta-analysis
batch-effect
updated 23 hours ago by
Ram
43k • written 9.9 years ago by
BrunoGiotti
▴ 120
6
votes
11
replies
3.3k
views
Collapsing probesets to genes on WGCNA
WGCNA
gene-expression
R
updated 2 days ago by
Ram
43k • written 5.2 years ago by
Davide Chicco
▴ 120
3
votes
4
replies
3.3k
views
Motif analysis of DMRs (Differentially Methylated Regions) by HOMER
next-gen
updated 8 days ago by
Ram
43k • written 6.7 years ago by
inschigu
▴ 10
1
vote
8
replies
3.3k
views
cutadapt error problem
next-gen
cutadapt
updated 22 days ago by
Ram
43k • written 5.6 years ago by
amitpande74
▴ 20
1
vote
3
replies
3.3k
views
How to calculate Differential Gene expression between samples with replicates
Differential-Gene-Expression
RNA-Seq
updated 10 days ago by
Ram
43k • written 7.8 years ago by
doncheng1
• 0
0
votes
3
replies
3.2k
views
Batch correction (mass spectrometry data)
Combat
R
SVA
Biostatistics
batch-effect
updated 23 hours ago by
Ram
43k • written 7.4 years ago by
mkhadka10
• 0
1
vote
4
replies
3.1k
views
remove batch effect for multiple tumor data
RNA-Seq
batch-effect
updated 23 hours ago by
Ram
43k • written 7.1 years ago by
hellocita
▴ 40
2
votes
1
reply
3.1k
views
Batch effect correction in DE analysis of single cell RNA-seq data and visualization
Seurat
Batch-effect
SCDE
RNA-Seq
Limma
updated 2 days ago by
Ram
43k • written 5.5 years ago by
Poorya Parvizi
▴ 60
0
votes
1
reply
3.1k
views
Removing batch effects from RPKM data
limma
removeBatchEffect
batch-effect
rpkm
updated 2 days ago by
Ram
43k • written 8.5 years ago by
AB
▴ 360
0
votes
3
replies
3.0k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 23 hours ago by
Ram
43k • written 8.9 years ago by
siddharth.patel.153
• 0
0
votes
3
replies
3.0k
views
Is there any method for using WES data from Illumina Hiseq into ABSOLUTE?
R
next-gen-sequencing
absolute
updated 22 days ago by
Ram
43k • written 6.7 years ago by
namhaesly
• 0
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 1 day ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
8
votes
4
replies
3.0k
views
Read count correlation between samples
differential-gene-expression
RNA-seq
updated 10 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
3
votes
3
replies
3.0k
views
Quick way to Identify batch effect from covariates?
bioconductor
batch-effect
updated 23 hours ago by
Ram
43k • written 7.9 years ago by
James Ashmore
★ 3.4k
0
votes
2
replies
2.9k
views
Should I pre-normalize RNAseq data before combat?
RNA-Seq
combat
batch-effect
R
updated 2 days ago by
Ram
43k • written 4.8 years ago by
zhaoliang0302
▴ 50
1
vote
2
replies
2.9k
views
Taking surrogate variable into account before running PCA
sva
svaseq
batch-effect
updated 1 day ago by
Ram
43k • written 6.8 years ago by
wamiqsaifi
• 0
0
votes
1
reply
2.9k
views
Microarray batch effect correction
Microarray
Batch-effect
updated 23 hours ago by
Ram
43k • written 6.6 years ago by
sarahmanderni
▴ 100
2
votes
5
replies
2.8k
views
Batch effect in Axiom Human Origins Array
affymetrix
array
batch-effect
updated 2 days ago by
Ram
43k • written 7.9 years ago by
Simo
▴ 50
0
votes
0
replies
2.8k
views
TCGA RNAseqVer2 batch effects
TCGA
RNA-Seq
batch-effect
updated 2 days ago by
Ram
43k • written 8.5 years ago by
annadv
• 0
1
vote
5
replies
2.8k
views
Batch effect identification using PCA
PCA
qRT-PCR
R
targeted-assay
Batch-Effect
updated 4 days ago by
Ram
43k • written 3.9 years ago by
mohammedtoufiq91
▴ 250
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 23 hours ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
1
vote
1
reply
2.8k
views
removing batch effects from large number of data sets
Microarray
batch-effect
updated 2 days ago by
Ram
43k • written 5.9 years ago by
nazaninhoseinkhan
▴ 520
5
votes
4
replies
2.8k
views
genefu for PAM50 prediction
RNA-Seq
breast cancer
subtyping
updated 2 days ago by
hamarillo
▴ 70 • written 5.6 years ago by
silviajserrano
▴ 50
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq
RNA-Seq
batch-effect
DESeq2
updated 2 days ago by
Ram
43k • written 5.1 years ago by
grant.hovhannisyan
★ 2.6k
0
votes
1
reply
2.8k
views
Can't make sva comparison despite very distinct batch effects
sva
batch-effect
updated 1 day ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
0
votes
4
replies
2.7k
views
MACS2 BAMPE and BEDPE gave dramatically different "mean fragment size"
ChIP-Seq
updated 25 days ago by
axol0tl
• 0 • written 6.5 years ago by
Xinwei Han
• 0
1
vote
1
reply
2.7k
views
Plotting a PCA Plot from SVASeq results
pca
ruvseq
sva
svaseq
batch-effect
updated 2 days ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression
RNA-Seq
GTex
DESeq2
updated 10 days ago by
Ram
43k • written 6.4 years ago by
vikram
▴ 10
2
votes
5
replies
2.7k
views
primer design to discriminate sequences in intron-exon MSA
primer
MSA
intron-exon
updated 13 days ago by
Amruta
• 0 • written 6.6 years ago by
Anand Rao
▴ 630
0
votes
0
replies
2.7k
views
Comparing lists generated by Counter() and .most_common() for AA seqs
python
amino-acid
updated 2 days ago by
Ram
43k • written 9.9 years ago by
st.ph.n
★ 2.7k
7
votes
3
replies
2.7k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 10 hours ago by
colindaven
6.3k • written 15 months ago by
Dr.Animo
▴ 130
3
votes
16
replies
2.7k
views
design matrix for dge
limma
differential-gene-expression
r
updated 10 days ago by
Ram
43k • written 7.9 years ago by
1234anjalianjali1234
▴ 50
7
votes
10
replies
2.6k
views
6 follow
Batch effect correction to compare differentially expressed genes across datasets
batch
batch-effect
DESeq2
rna-seq
updated 2 days ago by
Ram
43k • written 2.0 years ago by
mmitra
▴ 60
2
votes
4
replies
2.6k
views
DESeq2 inconsistent results
differential-gene-expression
RNA-Seq
DESeq2
updated 10 days ago by
Ram
43k • written 8.0 years ago by
Chris Gene
▴ 80
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 23 hours ago by
Ram
43k • written 9.1 years ago by
chengzhao41
▴ 110
4
votes
4
replies
2.6k
views
Advice on Handling Batch Effect in ChIP-seq Experiment
ChIP-Seq
batch-effect
sequencing
updated 2 days ago by
Ram
43k • written 4.6 years ago by
dmj6ab
▴ 20
1,000 results • Page
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Answer: Duplicate marking, read names, and the SRA
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Answer: Cellranger count error: Input FASTQ file ended prematurely
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
Answer: ClusterProfiler enrichKEGG – remove organism name in plots?
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Comment: Duplicate marking, read names, and the SRA
by
Luka
• 0
>In many cases those remain recoverable using the -F option when you dump the data (cloud download not required) The -F option (or any equ…
Answer: Duplicate marking, read names, and the SRA
by
GenoMax
141k
To be specific, not every dataset in SRA loses the original identifiers. In many cases those remain recoverable using the `-F` option when …
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
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43k
To use different versions of R and bioconductor, you don't really need RStudio. One can simply create new conda environments with the requi…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
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BioinfGuru
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Done. Thank you.
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GenoMax
141k
Perhaps add the word linux/ubuntu to the title? You have noted that the instructions are for Ubuntu in text.
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
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★ 1.7k
Thanks @Ram I'll add that to the intro. I'm the admin on my machine so I haven't found it necessary to install any other way. I'll try a fr…
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141k
No GPR files with this data unless you ask the submitters for them directly. You can find the matrix of data here: https://ftp.ncbi.nlm.nih…
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by
GenoMax
141k
That is odd. Thanks for following-up and providing an explanation.
Answer: Cellranger count error: Input FASTQ file ended prematurely
by
bp22
▴ 70
Dear all, The reason for the error was due to the index (I1) fastq files, for example `SI-GA-A1_1_S1_L001_I1_001.fastq.gz` having a lo…
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43k
Your tutorial required `sudo` and thus is not doable for a majority of people. Any alternative to `sudo snap`?
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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: …
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BioinfGuru
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https://help.galaxyproject.org/
Answer: RNA seq differential expression analysis
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Mohamed Abderrahmane
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The tool RSEM, which performs transcript quantification for RNA-Seq data, provides FPKM.
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Enrique
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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…
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