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0 votes
0 replies
760 views
DiffBind Profile Plot Error
diffbind atac-seq
updated by GenoMax GenoMax • written by B.N. • B.N.
3 votes
0 replies
614 views
Tool: I Built a Simple Website to Help Students Find Research Labs
students career research academia web-application
written by bitsofadventures • bitsofadventures
0 votes
0 replies
560 views
Bacterial annotators: chromosomes, plasmids, integrons, prophages ?(and other mobile element)
integrons chromosomes plasmids
updated by GenoMax GenoMax • written by psuazosoto • psuazosoto
6 votes
8 replies
6.5K views
Tool: New ultraperformant version of SICER/epic: epic2
chip-seq
updated by GenoMax GenoMax • written by endrebak852 • endrebak852
0 votes
2 replies
1.4K views
bcftools/vt split multiallelics - split GT along with splitting multi-allelics
multiallelics decompose bcftools vcf vt
written by Ram Ram
0 votes
4 replies
1.3K views
VCF filter by read depth
vcf
updated by Ram Ram • written by shu8 • shu8
0 votes
0 replies
749 views
Volcano Plot and DGE analysis
dge volcano-plot scrna-seq
updated by Ram Ram • written by JuanJo • JuanJo
1 vote
1 reply
692 views
only ~12% of assigned reads on featurecount
rna-seq
updated by DGTool • DGTool • written by diogo.moraes • diogo.moraes
1 vote
1 reply
1.1K views
Where can I find a database of healthy genotypes as well as a database of genetic diseases to link these data?
snpid database genotypes
updated by Jeremy Leipzig Jeremy Leipzig • written by Crypto • Crypto
1 vote
3 replies
4.1K views
Weird behaviour - WGCNA hub analysis results in Cytoscape through CytoHubba plugin change every time I run it!
rnaseq wgcna cytoscape hubs cytohubba
updated by xanderpico xanderpico • written by Raito92 Raito92
1 vote
5 replies
3.1K views
UMItools dedup deduplication taking too much time + RAM
umi-tools bam rna-seq
updated by i.sudbery i.sudbery • written by lluc.cabus • lluc.cabus
0 votes
0 replies
516 views
iMAT (integrative metabolic análisis tool) - MATLAB
imat matlab
updated by Ram Ram • written by debocolman • debocolman
0 votes
1 reply
956 views
Does vg provides an api?
cpp vg api
updated by Jordan M Eizenga • Jordan M Eizenga • written by guntul • guntul
0 votes
2 replies
728 views
Aligning a genome with a size of about 300,000.
alignment snapgen genome
updated by GenoMax GenoMax • written by trezini • trezini
0 votes
1 reply
824 views
Similar tools to visualize pileup of long-read alignments to a STR locus
str long-reads pileups nanopore
updated by WouterDeCoster WouterDeCoster • written by Antonio • Antonio
2 votes
1 reply
704 views
What is trait discoverability?
snp phenotype gene trait
updated by GenoMax GenoMax • written by _quantum_girl_ • _quantum_girl_
0 votes
0 replies
806 views
Salmon transcript-level to gene-level quantification
r salmon rna-seq
written by Mitmischer • Mitmischer
1 vote
1 reply
1.1K views
SNP Density plot with custom genome using karyoploteR
ngs snp r
updated by zx8754 zx8754 • written by adarsh • adarsh
0 votes
2 replies
1.4K views
Need help with AUGUSTUS and AGAT for gene prediction and feature extraction, respectively.
augustus agat annotation genome agat
updated by Juke34 Juke34 • written by Vijith • Vijith
0 votes
3 replies
1.1K views
Detection of unknown sub cells in a population of cells using DEGs from scRNAseq data
scrnaseq
updated by ATpoint ATpoint • written by ashkan ashkan
0 votes
5 replies
2.3K views
Decision on Upregulated/Downregulated Genes in DE list- P-value and Log fold change
pvalue logfoldchange
updated by Mensur Dlakic Mensur Dlakic • written by odi • odi
0 votes
24 replies
5.1K views
TCGA Biolinks code issue
normalization tcgabiolinks
updated by mazegriff • mazegriff • written by nuorain • nuorain
0 votes
3 replies
2.1K views
Error in pheatmap 'Error in hclust(d, method = method) : must have n >= 2 objects to cluster' for selected genes
pheatmap
updated by Mensur Dlakic Mensur Dlakic • written by aackermann287 • aackermann287
0 votes
5 replies
1.2K views
MarkDuplicatesSpark throwing disk quota errors
gatk
written by ChumBucket2024 • ChumBucket2024
0 votes
0 replies
612 views
Linear Mixed-effects Modelling for Mouse Tumor Growth Data
lmertest modelling mixed-effects lme4
written by BioNovice247 • BioNovice247
1 vote
4 replies
2.2K views
Cannot process a custom VCF file using bcftools
r bcftools vcf
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Qiong • Qiong
0 votes
1 reply
649 views
filter genes for differential gene expression
rna-seq differential-gene-expression
updated by Ram Ram • written by bleven • bleven
1 vote
0 replies
969 views
Best Practices for Tumor-Only WES Data Analysis: Seeking Feedback on Variant Calling Pipeline
gatk mutect wes cancer
written by George • George
0 votes
0 replies
620 views
CODEX/Phenocycler -> QuPath -> Seurat pipeline basic help needed
qupath codex seurat phenocycler
written by yura.grabovska • yura.grabovska
0 votes
1 reply
1.0K views
How to compare SNPs in different population
snps genome vcf
updated by dthorbur dthorbur • written by Elisa • Elisa
0 votes
0 replies
603 views
News: RADseq data analysis using Stacks (online course)
radseq phylogenomics population-genomics stacks
updated by Ram Ram • written by Physalia-courses Physalia-courses
0 votes
2 replies
1.3K views
KEGG MAPPER Reconstruct
kegg mapper
updated by andres.firrincieli andres.firrincieli • written by Julián • Julián
1 vote
6 replies
1.7K views
RNA-Seq multiple lane
bam rna-seq transcriptomics
written by MaxMin • MaxMin
0 votes
4 replies
1.4K views
Problems with Megahit wanting to overwrite the Input for the output directory
metagenomics megahit slurm
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Jan • Jan
0 votes
6 replies
2.1K views
Pheatmap cluster by columns not working
r pheatmap
written by Nona • Nona
0 votes
5 replies
2.3K views
error when installing gistic2 using conda
conda gistic2
updated by bioruffo • bioruffo • written by luckyday1661 • luckyday1661
0 votes
2 replies
1.0K views
LOC gene on opposite DNA-strand causes lower log2FC value?
genes loc bulk-rna-seq
updated by colindaven colindaven • written by Biomed-jeh • Biomed-jeh
1 vote
0 replies
482 views
How to determine the origin of replication of plasmid
plasmid
written by Bruntland Aldre • Bruntland Aldre
0 votes
4 replies
1.8K views
genome assembly records not present in assembly_summary.txt
ncbi bacteria assembly
updated by ajmalpdrc • ajmalpdrc • written by sapuizait • sapuizait
0 votes
3 replies
1.0K views
The best tool for Scaffolding
contigs scaffold assembly spades
updated by dthorbur dthorbur • written by davidmaimoun • davidmaimoun
0 votes
2 replies
1.2K views
Assembly Question
question flye contig assembly
updated by ajmalpdrc • ajmalpdrc • written by parb2182 • parb2182
0 votes
5 replies
1.7K views
Best Way to Assemble DNA Sequencing Data
dna-sequencing assembly
updated by ajmalpdrc • ajmalpdrc • written by echolley • echolley
0 votes
3 replies
1.2K views
SPAdes for specific strain assembly from stool sequenced data
assembly spades fastq
updated by dthorbur dthorbur • written by chemokine-1 • chemokine-1
0 votes
3 replies
1.7K views
Cross-strand correlation for paired-end ChIP-seq data
paired-end chip-seq relcc single-end
updated by LChart LChart • written by alison.ludzki • alison.ludzki
0 votes
3 replies
1.1K views
Error with filterbytile.sh from BBMap suite
quality control reads
written by SHIRUI • SHIRUI
0 votes
2 replies
1.3K views
RMSD value greater than backbone
docking rmsd md molecular simulation
updated by aUser • aUser • written by Tiara • Tiara
2 votes
0 replies
1.3K views
Tool: Neurosnap Tools: New Fully Open Source Package For Molecular Biology
msa protein docking ligand pdb
written by keaun • keaun
0 votes
2 replies
905 views
Matrix for a Fisher's exact test
p-value fishers-test
updated by stu.tug • stu.tug • written by Adelya • Adelya
0 votes
3 replies
1.0K views
Help With Sleuth
sleuth rnaseq
updated by dsull dsull • written by Rangarajan • Rangarajan
0 votes
3 replies
1.1K views
ballgown shows very different results depending on number of groups prepared with hisat2-stringtie
ballgown stringtie
written by thomas.heigl.ibk • thomas.heigl.ibk
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