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0 votes
1 reply
802 views
PbJelly Resume
gap-filling pacbio pbjelly
updated by eileenbaptista • eileenbaptista • written by Lissa Cruz Saavedra • Lissa Cruz Saavedra
0 votes
0 replies
540 views
How do I figure out which chain a ligand is bound to using rcsb-api?
rcsb
updated by GenoMax GenoMax • written by Priyal • Priyal
1 vote
2 replies
942 views
Deseq2
pydeseq2 deseq2
updated by GenoMax GenoMax • written by sk_24 • sk_24
0 votes
0 replies
1.0K views
News: In-Person NGS Epigenomics Workshop (November 3-5 in Munich, Germany)
chipseq bisulfiteseq atacseq workshop
written by ecSeq Bioinformatics • ecSeq Bioinformatics
1 vote
0 replies
1.0K views
News: Announcing a New Journal – Bioinformatics Methods and Applications – Now Open for Submissions
bioinformatics
written by Wei • Wei
0 votes
1 reply
764 views
How to address conflicting circRNA expression results between public datasets and published studies? is it normal?
cicrna-geo
updated by rfran010 • rfran010 • written by ParastooA • ParastooA
0 votes
6 replies
1.3K views
Help for Pooled Exome Sequencing SNP Analysis
gatk snp exome polymorphisms
written by alejandro.mejiam1 • alejandro.mejiam1
0 votes
0 replies
557 views
low variant sites similarity between linear reference and vg call path
call vg
updated by GenoMax GenoMax • written by PolenP • PolenP
0 votes
0 replies
782 views
KEGG pathways. How to plot the log2FC of genes collapsed into a "node"?
visualization deg kegg r pathway
written by txema.heredia • txema.heredia
0 votes
5 replies
1.4K views
MACS3 Parameter adjustments
human libraries illumina callpeak macs3
written by María José • María José
0 votes
1 reply
1.2K views
DeSeq2 how to change design matrix when samples are exclusive: error in “Model matrix not full rank” checkFullRank(full)
deseq2
updated by ATpoint ATpoint • written by totoroGirl • totoroGirl
0 votes
1 reply
763 views
Interactive UMAP scanpy
umap scanpy interactive
updated by antonioggsousa antonioggsousa • written by npont • npont
1 vote
5 replies
2.0K views
Can I use removeBatchEffect() before performing DEG analysis in bulk RNA-seq with limma-voom?
batchcorrection voom deganalysis limma bulkrna
updated by i.sudbery i.sudbery • written by Sumeet • Sumeet
1 vote
5 replies
1.3K views
Log2FC track Visualization in IGV
visualization igv rnaseq
written by SomeOne • SomeOne
0 votes
0 replies
842 views
News: online course: Sex Chromosome Evolution - 6–10 October 2025
sexchromosome evolution genomics
written by Physalia-courses Physalia-courses
0 votes
0 replies
534 views
GSEA of sugarcane
gsea
written by Bushra Bibi Bushra Bibi
0 votes
6 replies
1.8K views
DESeq2 design for differential expression with 2 timepoints and 2 controls
transcriptomic feeding deseq2 rnaseq
updated by txema.heredia • txema.heredia • written by Cristina • Cristina
0 votes
12 replies
2.1K views
FeatureCount : Successfully assigned alignments is low
rnaseq featurecount
written by HarperReed • HarperReed
0 votes
2 replies
1.2K views
Difficulties in calling peaks for CUT&RUN (IgG control with high RPKM value)
cutrun calling igg peak
written by Basti • Basti
0 votes
3 replies
1.3K views
custom BED to UCSC genome browser
browser ucsc ucsc-genome-browser genome methylation bed
written by npont • npont
0 votes
2 replies
857 views
unmatched number of reads after trimming treatment by afterqc
ngs genome assembly
written by 德水 • 德水
0 votes
1 reply
775 views
Extract Specific RNA-seq reads from BAM using deeptools
rna-seq deeptools
updated by GenoMax GenoMax • written by Qilin • Qilin
0 votes
11 replies
2.1K views
Error Correction with Tadpole and BBMerge
bbmerge tadpole error correction
written by Jon • Jon
0 votes
1 reply
790 views
Quantification for small RNAseq data
quantification seq data smallrna
updated by rfran010 • rfran010 • written by ZuelTech • ZuelTech
1 vote
4 replies
2.2K views
GrCh37 or GrCh38? That is the question.
grch37 sequence human genome grch38
written by Anjan Anjan
0 votes
2 replies
1.1K views
Scvi - Integration
integration singlecell scvi
written by t.fosk • t.fosk
0 votes
3 replies
1.0K views
Bootstrapping in RNA-seq
bootstrapping rnaseq
updated by rfran010 • rfran010 • written by littlebioinformatician • littlebioinformatician
0 votes
2 replies
1.1K views
Computing ka/ks ratio for individual genes.
ks ka evolution selection
written by Shakunthala Natarajan • Shakunthala Natarajan
1 vote
0 replies
2.0K views
Job: Several Permanent Positions as Bioinformatician/Computational Biologist/System Developer/Project Leader at Swedish national research infrastructures
sweden scilifelab genomics uppsala proteomics
written by Matthias Zepper Matthias Zepper
1 vote
2 replies
839 views
Obtaining a BED/GTF from Ensembl
rna-seq ensembl bcftools rna
written by joe_genome • joe_genome
0 votes
0 replies
967 views
News: New Bioconductor and Physalia Collaboration!
bioconductor dataanalysis genomics
written by Physalia-courses Physalia-courses
0 votes
1 reply
910 views
Read1 and read2 asymmetry in stranded, paired-end rnaseq data aligned by STAR
stranded star rnaseq antisense sense
updated by rfran010 • rfran010 • written by yampolsk • yampolsk
0 votes
1 reply
1.2K views
Does the order of SplitNCigarReads and MarkDuplicates affect RNA-seq variant calling results?
variantcalling. rnaseq gatk
updated by rfran010 • rfran010 • written by iamsmor • iamsmor
0 votes
0 replies
598 views
Should I standardize age and age2 as covariates in GWAS models?
gwas covariates
written by yu • yu
0 votes
6 replies
1.3K views
Venn Diagram
venndiagram
updated by lieven.sterck lieven.sterck • written by Nasim Gandomdoust • Nasim Gandomdoust
0 votes
1 reply
687 views
PhageTerm error
phage genome phageterm assamble
updated by GenoMax GenoMax • written by NIkita • NIkita
0 votes
1 reply
765 views
WGCNA Workflow from GEO FASTQ Files – Expression Type, Sample Inclusion, and Preprocessing
fastq wgcna rna
updated by GenoMax GenoMax • written by tutorwhizzz • tutorwhizzz
0 votes
0 replies
519 views
small RNA-Seq pipeline Standstill
ngs mirna
written by anthony.santana.703.j • anthony.santana.703.j
0 votes
3 replies
915 views
Construct correct contrast
contrast model-matrix design-matrix
written by jkim • jkim
0 votes
0 replies
485 views
piRNAs Analysis Pipelines
pirnas smallrna
written by GA • GA
0 votes
1 reply
970 views
Beagle PATH (partially) recognised on Ubuntu 22.04
ubuntu beagle beast mcmc
updated by GenoMax GenoMax • written by Luca Arbore • Luca Arbore
0 votes
0 replies
548 views
CNV Computation with HoneyBadger
cnv honeybadger
updated by GenoMax GenoMax • written by mete.han.celebi • mete.han.celebi
0 votes
0 replies
642 views
How to predict programatically TFBS and calculate PWM Score as JASPAR
pwmscan tfbs jaspar
written by t.kajiyama • t.kajiyama
0 votes
14 replies
2.2K views
Host Removal Issues Human/Dog with samples containing Eukaryotic species
mapping eukarotic host
updated by Ram Ram • written by Jon • Jon
0 votes
1 reply
1.1K views
Pharokka Error
error annotating viral pharokka genome
updated by Mensur Dlakic Mensur Dlakic • written by NIkita • NIkita
1 vote
0 replies
620 views
Combining Metatranscriptomics (Mtx) and Metagenomics (Mgx)
metagenomics reference-based metatranscriptomics alignment
updated by GenoMax GenoMax • written by rk009 • rk009
0 votes
1 reply
777 views
how to make a circular plot of variants
circular plot
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Bushra Bibi Bushra Bibi
0 votes
6 replies
1.4K views
GSEA analysis
rna-seq rna analysis
updated by GenoMax GenoMax • written by Ahmed • Ahmed
0 votes
1 reply
677 views
how to make go term plot and kegg pathway plot using InterProScan output
interproscan
written by Bushra Bibi Bushra Bibi
1 vote
3 replies
1.3K views
Why little difference in RNAseq alignment when flipping forward and reverse strand with paired end reads
mrna rna-seq bowtie alignment
updated by swbarnes2 swbarnes2 • written by JourneyToAbyss JourneyToAbyss
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