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0 votes
2 replies
1.4K views
snpEff: Unsupported structural variant types
vcf snpeff
written by shpak.max 8
0 votes
1 reply
1.5K views
How to pull specific comparisons for DEGs in DESeq2? Trying to understand setting contrasts after the model matrix and results lists.
deg rnaseq deseq2
updated by ATpoint 9.1K • | written by atan 0
0 votes
4 replies
2.2K views
Feature Counts vs Salmon quantification
featurecounts salmon rna-seq star
updated by GenoMax 16K • | written by rajdeepboral00 7
1 vote
3 replies
3.0K views
DESeq2 Glimma2 visualisation error
deseq2 glimma2 plot r
updated by atakanekiz 33 • | written by Pahi 3
0 votes
1 reply
885 views
Generate density plot for methylation data
methylation wgbs
updated by cmdcolin 448 • | written by ty.fu 0
0 votes
0 replies
670 views
News: RNA-Seq Analysis
rna-seq
updated by ATpoint 9.1K • | written by oliverhooker 14
0 votes
0 replies
651 views
News: Introduction to Python for Ecologists and Evolutionary Biologists
python
updated by ATpoint 9.1K • | written by oliverhooker 14
0 votes
5 replies
2.5K views
Cellranger error
10x multiplexing single cell
updated by GenoMax 16K • | written by zizigolu 438
0 votes
0 replies
612 views
Forum: computer science (undergrad) interested in starting a portfolio showcasing informatics skills
beginner
written by lesalgado 0
1 vote
6 replies
2.9K views
Comparison of different RNAseq data sets
batch-effect deg rnaseq
written by DrSmad 1
0 votes
0 replies
705 views
Low correlation from SparCC when using relative abundance tables.
network microbiome
written by yesquokkan 1
0 votes
3 replies
2.6K views
how to do Manhatton plot for significant DNA methylation sites associations
r array epic statistics epigenetics
updated by Đorđe 2 • | written by Bioinfonext 48
0 votes
2 replies
1.3K views
ONT MinION QC: Concatenate or Analyze Individually
ont fungus fastqc
written by Acervo 0
0 votes
2 replies
1.5K views
Negative Results in McDonald–Kreitman MK test results
mktest
written by 18d10fee 0
0 votes
2 replies
1.1K views
Importing Mothur into Phyloseqs cons.taxonomy error
mothur phyloseq 16s
updated by GenoMax 16K • | written by jahlen.pinelo 0
0 votes
2 replies
1.2K views
Statistics
bh correction p-value significance scoary
updated by andres.firrincieli 412 • | written by erinda 1
1 vote
3 replies
2.1K views
Why did the QV value decrease significantly after using YAHS for HiC scaffolding?
merqury scaffolding assembly hic
updated by samuel.a.odonnell 86 • | written by xinguok794 1
0 votes
4 replies
7.9K views
How to submit a bacterial (endosymbiont) ITS rDNA sequence to GenBank?
its genbank
updated by Kevin Blighe 9.0K • | written by dce1ee77 0
0 votes
3 replies
8.0K views
vg input and output files
vg
updated by Kevin Blighe 9.0K • | written by Michael 0
0 votes
4 replies
7.6K views
Issue with renaming genes in expression matrix for heatmap in R
hetmap
updated by Kevin Blighe 9.0K • | written by Kelly 2
0 votes
3 replies
7.1K views
Genome assambly and annotation for isolated bacteria
reference dna wgs bacteria annotiton
updated by Kevin Blighe 9.0K • | written by m90 3
0 votes
4 replies
7.2K views
Midpoint rooting IQTREE newick file moves node support around
iqtree phylogeny ggtree phangorn ape
written by Luca Arbore 1
0 votes
2 replies
6.8K views
Reading AD and other genotype information from the VCF file
r vcf
updated by Kevin Blighe 9.0K • | written by ramiro.barrantes 6
0 votes
8 replies
12K views
Several questions for genereating human genome assembly
dorado genome assembly hifiasm
updated by colindaven 844 • | written by tungsega 1
0 votes
3 replies
6.8K views
Tool 'sra_source' does not exist.
galaxy
updated by Kevin Blighe 9.0K • | written by Atefeh 0
0 votes
2 replies
5.9K views
Structural Clustering of Transmembrane Domains of Membrane Proteins
foldseek
updated by Kevin Blighe 9.0K • | written by William 0
0 votes
4 replies
6.3K views
Power analysis for miRNA sequecing
power mirna analysis
updated by Kevin Blighe 9.0K • | written by abedkurdi10 19
0 votes
5 replies
7.9K views
single cell: differential expression between cluster subsets
scrna-seq statistics seurat
updated by Kevin Blighe 9.0K • | written by Lee 0
0 votes
3 replies
2.0K views
How to Calculate Average Coverage and Depth from ONT Sequencing
coverage average depth
updated by GenoMax 16K • | written by dheeraj 0
0 votes
6 replies
2.5K views
Finding differences between individual patients in a time-series RNA-seq?
rnaseq deseq2 dge
written by txema.heredia 31
2 votes
7 replies
8.8K views
How to Identify Conserved 21-mers Across TE Insertions in Drosophila?
consensussequence sequencealignment conservedmotifs rnai transposableelements
written by manikin_python9f 2
0 votes
9 replies
3.4K views
My PCA plot is weird: PC1 with 98.684% variance and PC2 with 0.582% variance
r pca rna-seq visualization
updated by Kevin Blighe 9.0K • | written by undergrad_student 1
0 votes
8 replies
14K views
Low Mapping Rate with Kallisto on RNA-seq Data
rnaseq mapping ratio kallisto low
updated by Kevin Blighe 9.0K • | written by meetmet 1
0 votes
4 replies
2.1K views
Randomizing train-test data split for classification tasks.
split rnaseq test train
written by Shakunthala Natarajan 2
0 votes
7 replies
2.1K views
Missing required field on nf-core/sopa
nf-core sopa
updated by Maxime Garcia 41 • | written by jomagrax 4
0 votes
0 replies
621 views
News: Course: Flow Cytometry data analysis with R/Bioconductor - online, 2-4 February
r cancer-genomics flow-cytometry bioconductor
written by Physalia-courses 281
0 votes
7 replies
8.1K views
Need help in Single cell proteomics data analysis
single cell
updated by Gordon Smyth 916 • | written by Saber_J 2
0 votes
5 replies
9.1K views
Best way to do protein structure guided similarity search?
alphafold blast structure proteins
updated by yl759 12 • | written by Mark 6
1 vote
6 replies
8.7K views
Variant analysis for mouse WES
variant-calling maftools vcf genome wes
updated by Kevin Blighe 9.0K • | written by alba 1
0 votes
5 replies
9.9K views
Whole Genome Sequencing IG regions
immunoglobulin wgs
updated by Kevin Blighe 9.0K • | written by 719 0
1 vote
4 replies
8.5K views
Subsetting before QC in Spatial Transcriptomics
spatial-transcriptomics rare-cell-types quality-control
written by Kent 3
0 votes
2 replies
7.5K views
How to get a legend from genoplotR?
visualization fastani genome genoplotr
updated by Kevin Blighe 9.0K • | written by marongiu.luigi 79
0 votes
5 replies
7.6K views
Trouble when installing arb
arb
updated by Kevin Blighe 9.0K • | written by krmoon518 3
0 votes
4 replies
7.1K views
Help with species tree with orthofinder, iqtree and branch labeling
iqtree trimal cafe5 orthofinder mafft
written by san96 19
0 votes
3 replies
5.7K views
Chimera removal dilemma in 16S V3–V4: necessary when using Kraken2/Bracken?
16s v3-v4 qiime2 kraken2 bracken
updated by GenoMax 16K • | written by Christopher 1
0 votes
4 replies
3.7K views
Functional prediction for proteins of bacteria.
predection proteins fuctional bacteria
updated by Kevin Blighe 9.0K • | written by m90 3
0 votes
3 replies
2.4K views
Genome Contamination Check with Blobtools
diamond blobtools genome blast
updated by Kevin Blighe 9.0K • | written by saamhasan55 3
0 votes
3 replies
2.1K views
help with modkit on nanopore sequencing data.
mokit nanopore help
written by felix.adams 0
0 votes
1 reply
1.1K views
Is this the correct order of steps in GATK germline cohort variant calling (VQSR workflow)?
gvcf vcf gatk vqsr
updated by Kevin Blighe 9.0K • | written by Ramnaresh 0
0 votes
1 reply
717 views
Forum: Seeking Advice on Bioinformatics Analysis for Atrasentan in IgA Nephropathy Research
bioinformatics atrasentan
updated by Ram 4.5K • | written by capafa1703 0
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