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896 results • Page 2 of 18
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7
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10
replies
2.8k
views
6 follow
Batch effect correction to compare differentially expressed genes across datasets
batch batch-effect DESeq2 rna-seq
updated 29 days ago by 43k • written 2.1 years ago by ▴ 60
7
votes
6
replies
1.3k
views
using different microarray datasets (meta-analysis?) for DEG pipeline
microarray meta-analysis DEG batch-effect
updated 28 days ago by 43k • written 4.9 years ago by ▴ 30
6
votes
11
replies
3.4k
views
Collapsing probesets to genes on WGCNA
WGCNA gene-expression R
updated 28 days ago by 43k • written 5.3 years ago by ▴ 120
6
votes
2
replies
1.5k
views
Writing a batch script for analyzing RNA-Seq data
RNA-Seq quantification alignment
updated 29 days ago by 43k • written 5.2 years ago by ▴ 250
6
votes
4
replies
1.6k
views
RNA-Seq: X samples and X batches
RNA-Seq edgeR DESeq2 Batch-Effect
updated 28 days ago by 43k • written 5.3 years ago by ▴ 40
6
votes
8
replies
659
views
BRAKER3 genome annotation
annotation BRAKER3 genome
updated 28 days ago by 14k • written 4 weeks ago by ▴ 40
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma microarray DEA batch-effect
updated 28 days ago by 43k • written 4.7 years ago by ▴ 60
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat RNA-Seq Limma DESeq2 batch-effect
updated 27 days ago by 43k • written 5.0 years ago by ▴ 140
6
votes
4
replies
431
views
Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
13 days ago by Estevão ▴ 10
6
votes
2
replies
234
views
EdgeR - relationship between logFC and coefficients
differential-expression r edger
updated 5 days ago by ★ 7.2k • written 5 days ago by ▴ 10
6
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon human bed v7 agilent all sureselect
updated 10 days ago by ▴ 10 • written 2.0 years ago by • 0
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing coverage
19 hours ago by Arton ▴ 10
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 3 days ago by • 0 • written 6.7 years ago by • 0
6
votes
4
replies
2.3k
views
Is there a way to get RNAFold output for multifasta in tabular format?
RNAFold
updated 28 days ago by • 0 • written 4.6 years ago by ▴ 40
6
votes
17
replies
6.6k
views
Can you add a label key to heatscatter plot in R?
heatscatter visualization R
updated 28 days ago by 43k • written 9.6 years ago by ▴ 100
6
votes
3
replies
225
views
Interpretting IGV output
IGV
updated 23 days ago by 8.7k • written 23 days ago by ▴ 50
6
votes
7
replies
369
views
Longest transcript variant per gene
transcript longest variant orthofinder
3 days ago by sansan_96 ▴ 90
6
votes
4
replies
13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic paired-end
updated 4 days ago by • 0 • written 6.4 years ago by ▴ 130
6
votes
0
replies
2.6k
views
Tool: Immuno-Navigator, a batch-corrected database for gene coexpression in the immune system
gene-co-expression batch-effect immunology
updated 27 days ago by 43k • written 7.1 years ago by ▴ 80
5
votes
2
replies
1.1k
views
How to perform batch correction when we have only single condition?
sva combat batch-effect DESeq2
updated 29 days ago by 43k • written 3.8 years ago by ▴ 680
5
votes
3
replies
755
views
Illumina reads preprocessing best practice for snp calling applications
Illumina snp
updated 26 days ago by • 0 • written 10 months ago by ▴ 310
5
votes
13
replies
1.9k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 25 days ago by 82k • written 26 days ago by ★ 1.7k
5
votes
4
replies
711
views
How to compare the quality of assemblies
nextdenovo assembly hifiasm pacbio
21 days ago by kirillkirilenko ▴ 40
5
votes
4
replies
2.9k
views
genefu for PAM50 prediction
RNA-Seq breast cancer subtyping
updated 29 days ago by ▴ 70 • written 5.7 years ago by ▴ 50
5
votes
2
replies
359
views
Forum: Bioinformatics: Where do I start
Sequencing
updated 29 days ago by 43k • written 29 days ago by ▴ 20
5
votes
4
replies
715
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq EdgeR DEGs DESeq2
27 days ago by BioinfGuru ★ 1.7k
5
votes
5
replies
2.2k
views
batch effect in RNAseq analysis using tophat cufflinks pipeline
RNA-Seq tophat batch-effect cufflinks
updated 28 days ago by 43k • written 5.4 years ago by • 0
5
votes
2
replies
343
views
ChIP-seq datasets: input samples omitted?
ChIP-seq Normalization NGS
updated 16 days ago by 19k • written 19 days ago by ▴ 40
5
votes
6
replies
583
views
Programmatically retrieving positions of protein active site residues
Uniprot PDB Proteins
updated 15 days ago by ▴ 760 • written 16 days ago by ▴ 40
5
votes
5
replies
309
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA DADA2 metabarcoding
updated 13 days ago by ▴ 30 • written 13 days ago by ▴ 150
5
votes
5
replies
302
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
7 days ago by Chris ▴ 280
5
votes
3
replies
311
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 15 days ago by ★ 1.2k • written 15 days ago by • 0
5
votes
2
replies
1.8k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq batch batch-effect sequencing
updated 29 days ago by 43k • written 3.0 years ago by ▴ 60
5
votes
6
replies
7.3k
views
scatter plot, aov()
aov scatter-plot anova
updated 28 days ago by 43k • written 3.2 years ago by ▴ 170
5
votes
4
replies
379
views
I'm new to cell ranger. Can single cells prepared with a protocol other than the 10x genomics protocol not be processed with cell ranger?
cellranger scRNA-seq 10x
29 days ago by Spring • 0
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 27 days ago by 43k • written 9.2 years ago by ▴ 110
5
votes
5
replies
656
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 12 days ago by • 0 • written 20 days ago by ★ 3.9k
4
votes
12
replies
4.9k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation Experience Illumina Mouse
updated 6 days ago by ▴ 180 • written 3.0 years ago by ▴ 20
4
votes
2
replies
373
views
Assume "yes" as the answer to any prompts with bioconda
docker container bioconda
updated 27 days ago by 8.6k • written 27 days ago by ▴ 20
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient molecule at bam DNA RG ends clipping damage
updated 7 days ago by ▴ 10 • written 2.5 years ago by • 0
4
votes
5
replies
448
views
Figures are disappeared from html report of SnpEff
HTML SnpEff
16 days ago by analyst ▴ 50
4
votes
9
replies
2.2k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing bowtie2 alignment samtools ngs
updated 12 days ago by • 0 • written 2.2 years ago by • 0
4
votes
1
reply
188
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
1 day ago by J. ▴ 40
4
votes
2
replies
274
views
GRCh38.gmap file
gnomix gmap
11 days ago by lorena9132 ▴ 10
4
votes
3
replies
2.2k
views
The result of differential gene expression analysis should be extracted based on adj.p.value ?
limma microarray bioconductor R
updated 28 days ago by 43k • written 6.4 years ago by ▴ 260
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome sequencing singleton SNP filter
updated 15 days ago by ▴ 20 • written 9.6 years ago by ▴ 40
4
votes
7
replies
628
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
16 days ago by e.r.zakiev ▴ 210
4
votes
6
replies
799
views
7 follow
Heatmap and rna-seq
RNA-Seq Heatmap
updated 18 days ago by ★ 6.0k • written 22 days ago by ▴ 10
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq RNA-Seq exon
updated 9 days ago by ▴ 30 • written 6.7 years ago by ★ 1.2k
4
votes
3
replies
434
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc conda nextflow
updated 18 days ago by 3.2k • written 19 days ago by ▴ 40
896 results • Page 2 of 18
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Answer: Using ggplotly in R
Comment: How to calculate coverage of Nanopore long read data?
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Calculate allelic frequency from VEP output vcf file
Answer: How can you *consistently* download BioProject IDs from NCBI's BioSample databas
Answer: Cluster sub-set analysis using Seurat
Answer: Cannot install bwa-mem2 via conda
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Recent Replies
Comment: Inquiry about deseq2 transformation by Chen • 0
that's helpful, thanks :)
Comment: bbmerge (bbmap) ~ error with insert size file output by Brian Bushnell 20k
Ah, this is a little embarrassing; those are the vectors for the neural network. I overloaded a field that was being used for the insert s…
Comment: Annotating file using bcftools by kl ▴ 10
Thanks - I corrected it. It doesn't seem to annotate. I converted to binary after which is what is shown below. It is not the output I want…
Comment: Filtering VCF files based on VAF giving incorrect results by Arton ▴ 10
These are valid questions. Does your code address the concerns you've raised? From what I understand, FilterVcf is primarily designed for h…
Answer: Calculate allelic frequency from VEP output vcf file by ramiro.barrantes • 0
Found the answer here!! https://github.com/Illumina/strelka/blob/master/docs/userGuide/README.md#somatic Although this leads to a str…
Comment: Using VEP annotation output as the input for a second VEP annotation by Ram 43k
That's not a valid reason to delete the post. If that information was sensitive, posting it here was a mistake in the first place. I don't …
Answer: In one PCA plot, can I calculate the percentage of different factors that contri by marco.barr ▴ 120
Hi, regardless of how you generated the data whether with DESeq2 or other pipeline, your differential expression matrix can be used as inpu…
Comment: Filtering VCF files based on VAF giving incorrect results by Pierre Lindenbaum 161k
> Do you think my commands were correct? I'm not familiar enough with this bcftools syntax. but what if there is no AD, what if both…
Answer: How can you *consistently* download BioProject IDs from NCBI's BioSample databas by Ash ▴ 10
I know this was asked several years ago, but finding this post helped me solve my own problem and in the process I solved this one too. …
Answer: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by swbarnes2 14k
Would Parkinson's be expected to have an effect on blood cells? Neurons, sure, but blood cells?
Comment: Doubt about the process of annotation, detection, identification and classificat by MarcosCosta • 0
Thank you very much, you've helped me a lot. Could you suggest a book or article that offers a complete explanation of these processes?
Comment: Filtering VCF files based on VAF giving incorrect results by Arton ▴ 10
Thank you. I can't try a completely new tool but I will keep your command for future use. Do you think my commands were correct? For exampl…
Comment: Add stats to boxplot in R by Ghada • 0
Thanks. Thats work
Comment: Genotyping sites with N in reference genome by Zhenyu Zhang ★ 1.2k
Whether N -> A/T/G/C represents a variant is heavily dependent on the tool itself, and I know most tools don't. Since you don't see it in y…
Comment: calculating genomic coverage/ base overlap in R by marco.barr ▴ 120
The code seems correct at first glance... How did you generate the data in the Excel file? Have you checked the exon annotations? You could…
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