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1 vote
1 reply
347 views
DESeq2 gives high sig gene number
deseq2 tcga
updated by ATpoint 9.1K • | written by Sara 1
0 votes
3 replies
389 views
How do I merge two overlapping rbcL FASTA fragments in BioEdit?
alignment chloroplast sanger
updated by lieven.sterck 1.6K • | written by alnus 0
0 votes
2 replies
559 views
BCLConvert 4.x behavior when Lane is omitted from [BCLConvert_Data] — per-lane defaults or single pool?
samplesheet bcl2fastq illumina sequencing bclconvert
written by Chaitanya 0
0 votes
0 replies
118 views
Best tool to orient a protein complex before SMD in GROMACS
moleculardynamics gromacs smd steeredmoleculardynamics orientation
written by rachana 0
1 vote
4 replies
1.4K views
Hello, I analyzed ONT 16S amplicon data using the EPI2ME workflow with Minimap2, but the output does not include representative FASTA sequences needed for downstream functional prediction with PICRUSt
epi2me picrust2 16s metagenomic ont
updated by Leonardo 1 • | written by Ramen 2
0 votes
1 reply
215 views
mismatch sites from GAM/GAF
vg
updated by colindaven 844 • | written by zhengluo 0
1 vote
3 replies
619 views
Is it normal and ok to observe symmetric PCA & heatmap when correcting paired samples for the patient ID?
differential-expression-analysis paired-deseq2
updated by i.sudbery 2.3K • | written by marieke 1
1 vote
1 reply
261 views
Statistical test for separation of groups in PCA and DESeq2 design with confounders
bulk rna desq2
updated by shannonNorgenBiotek 1 • | written by archanaverma433 2
0 votes
1 reply
397 views
Should I pool counts from the X and Y copies of pseudoautosomal genes when performing differential expression analysis?
pseudoautosomal differential-expression annotation
updated by Gordon Smyth 916 • | written by Ryan 0
0 votes
4 replies
709 views
Weak overlap of cell states of scRNAseq and Xenium data of the same samples
xenium
written by Beginner 9
0 votes
0 replies
280 views
Low-coverage NGS CNV: multiple chromosomes showing ~2.3 copy number with low confidence — mosaicism or normalization artifact?
pgt cnv
written by Alison 0
0 votes
2 replies
1.6K views
How do I compare two similar PPI networks using Cytoscape?
cytoscape string ppi networks
updated by Midsummer 0 • | written by gemmalouisebaldock 2
0 votes
2 replies
311 views
Forum: Complexity in reproduce the research work
bioinformatics researcher reproducibility
updated by Ram 4.5K • | written by Muhammad 0
0 votes
2 replies
307 views
Protein Homologous Sequences!
proteomics vaccinology immunoinformatics
updated by Ram 4.5K • | written by Muhammad 0
0 votes
4 replies
652 views
FindTransferAnchors error: "No features to use in finding transfer anchors" when using CELLxGENE `.h5ad` reference with Seurat
scanpy seurat scrnaseq findtransferanchors
written by VPs 1
0 votes
0 replies
160 views
News: (online course) Fundamentals of Biostatistics with R - 13–17 April
biomedicalresearch biostatistics epidemiology survivalanalysis
written by Physalia-courses 281
0 votes
0 replies
157 views
BLUPF90+....
blup
written by hwangseok1025 0
7 votes
0 replies
335 views
Tool: polars-bio - blazing fast Python DataFrames for genomic operations
genomics dataframes python polars
written by Marek 10
0 votes
1 reply
267 views
Exploring project idea
validation structural svs variants
updated by dthorbur 350 • | written by mustafa.kpn 1
0 votes
0 replies
190 views
tcga data analysis correlation between two signature
correlation signature gene tcga
written by jerko.ljubetic 0
0 votes
1 reply
333 views
Handling high missingness when merging single-sample VCFs
wgs ultima_wgs vcf merge
updated by samuel.a.odonnell 86 • | written by SeoG 1
1 vote
3 replies
530 views
metagenome binning with MetaBAT2, and Maxbin2 created bins for some samples but not others.
bacteria fungi metagenome binning
updated by Mensur Dlakic 3.0K • | written by Irshad 1
0 votes
1 reply
311 views
RNA_MUTECT_1.0_1 not working
variant tumor-only rna_mutect somatic
updated by DdogBoss 7 • | written by Charlotte Stubbe 0
0 votes
2 replies
422 views
Forum: MS CS after BS in Bioinformatics
csit
written by anasjamshed 14
0 votes
7 replies
3.4K views
Gene Set Enrichment Analysis with RNA-seq data
rna-seq next-gen r
updated by Gordon Smyth 916 • | written by deepak18 1
1 vote
3 replies
779 views
Tool: rsfgsea: Rust implementation of preranked GSEA built for large transcriptome workflows where GSEA became the bottleneck
rust python gsea tool fgsea
written by Denis Demin 3
2 votes
1 reply
411 views
Tool: Fast and Accurate DeepVariant on native Linux ARM64. Costs less than a piece of gum per genome
deepvariant arm64 variant-calling
updated by cmdcolin 448 • | written by antoniolamb 6
1 vote
5 replies
2.7K views
Extraction of read subsequences based on a region from a sam file
alignment sequence
updated by fravadona 0 • | written by gordon.freeman 1
0 votes
0 replies
167 views
News: (Online course) Metabarcoding in Microbial Ecology (16–20 March)
qiime2 metabarcoding r microbial-ecology
written by Physalia-courses 281
0 votes
2 replies
365 views
"Exome" probes designed off of mRNA sequences
capture exome sequencing
written by Shay 0
0 votes
0 replies
147 views
How to Interpret PHEWAS hits that are very rare but very significant?
frequency phenotype allele phewas p-value
written by joshua.rubin 0
0 votes
0 replies
268 views
Job: Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
genetics bioinformatics alzheimer omics
updated by GenoMax 16K • | written by belloy 1
0 votes
0 replies
244 views
Very high number of unique sequences in PacBio full-length 16S CCS data using DADA2
pacbio dada2 microbiome amplicon 16s
written by muhammad.ali 0
0 votes
1 reply
299 views
Phylogenetic tree construction
phylogenetic tree
updated by Michael Dondrup 5.6K • | written by Vishy001 0
0 votes
1 reply
1.1K views
Issues with FilterRNAMutationsNoPoN in RNA-Mutect Workflow for Tumour Mutational Burden Estimation
funcotator mutect2 tmb rna-mutect-wmn rna-mutect
updated by Charlotte Stubbe 0 • | written by kim 1
0 votes
3 replies
687 views
MM39 BED Files Genome Features
bed mm39
updated by GenoMax 16K • | written by joseph.landry 5
0 votes
0 replies
222 views
News: UConn CBC: de novo RNA-seq & scRNA-seq March workshops
scrnaseq workshop rnaseq training
written by bioadam 1
0 votes
4 replies
578 views
UCSC Genome Browser: Custom Data?
browser genome ucsc
written by Shane 0
0 votes
1 reply
413 views
V3V4 16s Sequencing, lots of merged reads that are too short
v3v4 16s dada2
updated by michael.ante 408 • | written by Emilie 1
0 votes
1 reply
352 views
Generating .rnk file for GSEA
gsea
updated by mbyvcm 48 • | written by Siobhan 0
0 votes
1 reply
529 views
Seurat v5 workflow for Integrated data
findallmarkers seurat dataintegration sctransform layers
updated by Arup Ghosh 402 • | written by _deb 0
0 votes
2 replies
488 views
High mapping failure (>80%) in clusterProfiler::bitr after HIPPIE–MCODE workflow
hippie cytoscape mcode
written by SD 0
6 votes
6 replies
3.1K views
Forum: GPU-enabled bioinformatics
gpu
updated by lestdnks 0 • | written by Dave Carlson 223
2 votes
1 reply
1.9K views
Tutorial: Fast SCENIC GRN Analysis with RegDiffusion
grn network scrna-seq wgcna
updated by lestdnks 0 • | written by Hao 3
0 votes
4 replies
587 views
RNA-seq - in-silico averaging of samples, comparison to true pooling
deseq2 pooling rna-seq
updated by swbarnes2 1.5K • | written by boczniak767 89
0 votes
0 replies
161 views
Deeptools ComputeMatrix returns 0 values for clearly populated regions
deeptools
updated by GenoMax 16K • | written by eglsidlauskaite 0
0 votes
4 replies
469 views
Ideal human immune sequence sets for generating blastp database
blast immune protein blastp
written by Alex Reynolds 3.6K
0 votes
0 replies
366 views
Job: Doctoral student in Computational Genomics, Gothenburg, Sweden
snp evolution genome machine-learning
written by sina.majidian 2
0 votes
2 replies
379 views
combat-Seq error
combat-seq r
updated by ATpoint 9.1K • | written by pinheirofabiano 14
0 votes
1 reply
517 views
Recommendations of tools for segmentation of 10x Xenium data in human brain
xenium spatial-transcriptomics imaging single-cell
updated by Bastien Hervé 680 • | written by yura.grabovska 94
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