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0 votes
7 replies
2.0K views
Can you suggest a protein PDB that has two chainst but only 50 total number of atoms?
protein pdb protein-databank
updated by Matthias Zepper Matthias Zepper • written by 4fzcgueyp5 • 4fzcgueyp5
0 votes
2 replies
1.5K views
Forum: VCF bulk handling
bcftools snpeff wgs vep vcf
written by Javier • Javier
0 votes
13 replies
3.0K views
RNAseq of primary tumor and metastases in two different organ
metastases rna-seq deg r
updated by BioinfGuru BioinfGuru • written by matteo.levorato • matteo.levorato
1 vote
1 reply
804 views
VEP annotation --per_gene allele choice
vep
updated by Ram Ram • written by atariw • atariw
1 vote
4 replies
2.3K views
Why number of interactions decreased in current string database for plasmodium
string interactions ppi
updated by damian.szk • damian.szk • written by rohitsatyam102 rohitsatyam102
0 votes
2 replies
929 views
Are GeneExpression Subtype annotations removed from TCGA-GBM?
tcga-gbm subtyping tcga
updated by Zhenyu Zhang Zhenyu Zhang • written by Apollonia • Apollonia
0 votes
1 reply
770 views
RNA seq normalization and gene gene correlation
rna-seq pearson-correlation vst
updated by Ram Ram • written by Fish • Fish
0 votes
0 replies
696 views
KaryoPlot: Gene coverage over centromeric regions
gene coverage centromere bedtools
written by Mary • Mary
0 votes
0 replies
697 views
Protein stability analysis
mutation analysis
written by marco.barr • marco.barr
0 votes
4 replies
1.5K views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
transcriptomics htseq-count rna-seq ngs hisat2
updated by BioinfGuru BioinfGuru • written by Morteza • Morteza
0 votes
1 reply
921 views
how to change the gene header names in a fasta file?
fasta bioawk awk seqkit
updated by Ram Ram • written by rj.rezwan • rj.rezwan
0 votes
1 reply
842 views
How do I get the 3bp sequence on either side of a co-ordinate
sam genomics sequencing
updated by Ram Ram • written by nrav58 • nrav58
0 votes
4 replies
2.5K views
Annotation using Pfam
annotation metagenomic protein pfam
updated by Mensur Dlakic Mensur Dlakic • written by Md Moinuddin • Md Moinuddin
2 votes
0 replies
618 views
Tool: pySEACR
peak-calling cut-and-run
written by Adam • Adam
1 vote
3 replies
1.4K views
Ensembl assembly choice for DNA reference with no combined primary assembly
alignment hisat2 rna-seq ensembl assembly
updated by GenoMax GenoMax • written by AHerik • AHerik
0 votes
0 replies
546 views
Multiple Spike-Ins
merip spike-in
written by Adam • Adam
0 votes
0 replies
453 views
Tools for Sequence Consensus
consensus-sequence bacteria
updated by Ram Ram • written by Reno • Reno
0 votes
0 replies
709 views
News: Online course: Meta-analysis in R
meta-analysis r
updated by Ram Ram • written by Physalia-courses Physalia-courses
0 votes
1 reply
989 views
Biopython Blastn Error: CPU usage limit was exceeded appears for certain files
sequences python blast
updated by GenoMax GenoMax • written by Phi • Phi
3 votes
4 replies
5.4K views
Motif analysis of DMRs (Differentially Methylated Regions) by HOMER
next-gen
updated by Ram Ram • written by inschigu • inschigu
1 vote
0 replies
754 views
phasing tumor long-reads
nanopore ont haplotag phasing tumor
written by eebloom • eebloom
0 votes
3 replies
2.1K views
10x GEX and ADT data analysis in Seurat
seurat scrna-seq adt cite-seq gex
updated by ATpoint ATpoint • written by gdfsnkfns • gdfsnkfns
0 votes
6 replies
2.2K views
Correcting coordinates in gff3 file
awk unix gff3 python
updated by Matthias Zepper Matthias Zepper • written by hulu • hulu
0 votes
4 replies
1.1K views
Questions about transfering wgs file to reference genome file
fasta cram genome
written by me • me
0 votes
2 replies
1.5K views
WGCNA
pca wgcna eigengene
written by rajasekargutha • rajasekargutha
2 votes
6 replies
2.9K views
CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRleFromGR(x, weight = weight, ignore.strand = ignore.strand): Seqlengths of x contains NA values!
gff3 genomicranges orfik genomicfeatures
updated by GenoMax GenoMax • written by Estefania • Estefania
0 votes
2 replies
1.5K views
Error when i use EVidenceModeler to do the genome annotation
evidencemodeler annotation genome
written by Wren • Wren
0 votes
3 replies
1.2K views
BLASTP web- <20aa peptides- interpreting results/ minimum E value?
blast peptide blastp alignment
updated by GenoMax GenoMax • written by neish • neish
0 votes
5 replies
1.9K views
Having trouble building VG in Ubuntu
vg
updated by Ram Ram • written by ayushm64 • ayushm64
0 votes
5 replies
4.6K views
Shannon vs Simpson for TCR diversity estimation
tcr shannon simpson
updated by ATpoint ATpoint • written by CY CY
1 vote
0 replies
626 views
News: Online Live Course: Introduction to Machine Learning in R
rstats tscourses rlang rproject
updated by Ram Ram • written by Transmitting Science communication • Transmitting Science communication
1 vote
0 replies
806 views
DESeq2 comparing timepoints within treatment and account for background control change
rnaseq deg deseq2
updated by Ram Ram • written by ian.will • ian.will
2 votes
0 replies
585 views
News: Online Course Generalised Additive Mixed Models (GAMM): modelling space-time correlation structures
gamm rlang rstats rproject
updated by Ram Ram • written by Transmitting Science communication • Transmitting Science communication
2 votes
0 replies
611 views
News: Online Course Introduction to Network Analysis and Modelling
python network-analysis
updated by Ram Ram • written by Transmitting Science communication • Transmitting Science communication
0 votes
3 replies
1.5K views
Merging vcf files with bcftools ([E::get_intv] Failed to parse TBX_VCF, was wrong -p [type] used?)
vcf tabix bcftools
updated by Pierre Lindenbaum Pierre Lindenbaum • written by giulia.cosenza • giulia.cosenza
0 votes
0 replies
634 views
Surrogate variable analysis for paired RNA seq experiment
sva rnaseq ruvseq
written by nhaus • nhaus
0 votes
3 replies
916 views
True variants selection
vcf bcftools
updated by dthorbur dthorbur • written by maevalefeuvre • maevalefeuvre
0 votes
1 reply
676 views
How to reveal real AF of variant if duplicates can't be removed (such as in amplicon-seq)
allele-frequency amplicon-seq
updated by Ram Ram • written by CY CY
0 votes
0 replies
645 views
Creating a BSgenome data package from a NCBI assembly - Virus
virus bsgenomeforge bsgenome r
written by JirMan • JirMan
0 votes
7 replies
4.7K views
KEGG analysis in R
kegg clusterprofiler zea-mays
updated by letizia.ottaviani • letizia.ottaviani • written by san96 • san96
0 votes
0 replies
810 views
BETA whether on the same scale when performing rank-based inverse normal transformation on the same type of phenotype data for two cohorts separately and conducting GWAS on the transformed data?
normal inverse transformation
written by Isaac • Isaac
1 vote
3 replies
1.8K views
Why is DESeq2 normalization making my top feature have identical values across samples?
deseq2 wgcna
written by DNAngel DNAngel
0 votes
2 replies
1.4K views
Creating a cytoscape bubble figure
cytoscape network go
written by Dave Carlson Dave Carlson
0 votes
3 replies
1.7K views
Disrupting a gene interaction network
cytohubba cytoscape sequences mrna
written by george • george
0 votes
1 reply
949 views
ClueGO is not showing custom data
cluego cytoscape
updated by Scooter Scooter • written by Nicolas • Nicolas
1 vote
7 replies
8.5K views
problem with HOMER findMotifsGenome.pl
homer atac-seq
updated by kaaz • kaaz • written by ste.lu ste.lu
1 vote
3 replies
1.7K views
Best genome browser for manual curation of gene structure(s)?
structure gene
updated by cmdcolin cmdcolin • written by William William
0 votes
7 replies
8.2K views
How do I plot several sns.clustermap heatmaps in a single figure?
python seaborn
updated by Wubin • Wubin • written by roy.granit roy.granit
0 votes
1 reply
753 views
Human Methylation Infinum Bead - probe to gene mapping
tcga pancan data
updated by Zhenyu Zhang Zhenyu Zhang • written by shrutidesai0208 • shrutidesai0208
1 vote
5 replies
8.2K views
Is it just me or has www.ensembl.org been broken for a while?
ensembl
updated by joshua.theisen • joshua.theisen • written by gene_biostars • gene_biostars
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