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1 vote
2 replies
1.2K views
Outlier after DEseq2 in meta-analysis
meta-analysis rna-seq outlier deseq2
written by a.stef.44 • a.stef.44
0 votes
0 replies
756 views
Optimizing mutect/sarek for somatic substitution variant calling
mutect2 tumor-normal sarek variant-calling
updated by Ram Ram • written by ramiro.barrantes • ramiro.barrantes
0 votes
2 replies
1.5K views
Appropriate minimum gene set size for gene set enrichment analysis
htsanalyzer gsea fgsea
written by Nona • Nona
0 votes
0 replies
605 views
News: Course - Introduction to the Analysis of Longitudinal Data in Biology Using R
longitudinal-data r epidemiology forecasting gene-expression
updated by Ram Ram • written by Physalia-courses Physalia-courses
0 votes
1 reply
723 views
missing data in ChromHMM
chromhmm
updated by LChart LChart • written by luminea • luminea
0 votes
1 reply
565 views
Help on encode accessions
encode
updated by GenoMax GenoMax • written by tsomakiank • tsomakiank
0 votes
14 replies
2.4K views
Choosing the best representative transcript for a gene
transcript
written by ZuelTech • ZuelTech
1 vote
1 reply
1.6K views
Seurat Xenium QC
r xenium spatial seurat
updated by Bastien Hervé Bastien Hervé • written by yura.grabovska • yura.grabovska
0 votes
4 replies
1.2K views
gtf files for various organism in ucsc
gtf
written by 1769mkc 1769mkc
0 votes
3 replies
1.2K views
PyMOL scripting with GPUs on LSF
pymol hpc pse lsf structure
updated by GenoMax GenoMax • written by noodle noodle
0 votes
2 replies
1.3K views
Cluster regions based on similar/dissimilar ChIP-seq signal profile across the whole region and not just overall mean signal.
clustering chip-seq deeptools
updated by Ming Tommy Tang Ming Tommy Tang • written by rls_08 • rls_08
0 votes
4 replies
1.5K views
What is wrong with my scripts?
r gdc tcgabiolinks bioconductor
updated by Ming Tommy Tang Ming Tommy Tang • written by nuorain • nuorain
0 votes
3 replies
1.2K views
cnvpytor run problem
cnvpytor
updated by yura.grabovska • yura.grabovska • written by hamideh • hamideh
0 votes
6 replies
2.3K views
PCA for count data
pca
written by QX • QX
2 votes
2 replies
965 views
cnv_facets run problem
r cnv_facets
written by hamideh • hamideh
0 votes
15 replies
2.9K views
Merge VCF files by chromosome and Across samples
gatk picard mergevcf vcftools
written by Maverick • Maverick
0 votes
0 replies
581 views
News: Genomic Data Visualisation in R (online course)
data-visualisation genomic-data r
written by Physalia-courses Physalia-courses
0 votes
9 replies
2.3K views
miRNA mapping with bowtie2 gives low alignment %
bowtie2 alignment mirna
written by Ant • Ant
0 votes
3 replies
1.8K views
What does fully overlapping supplementary alignments mean?
alignment nanopore minimap2
updated by Michael Dondrup Michael Dondrup • written by njornet • njornet
0 votes
6 replies
1.6K views
Germline variants in Cancer
cancer tumor-normal germline-variant
written by prs • prs
0 votes
7 replies
5.0K views
Unexplainable missing values in single cell Seurat object
seurat single-cell
updated by Ram Ram • written by Gerard • Gerard
0 votes
5 replies
2.6K views
why do I get this error while reading single cell RNA seq data in R
scrna-seq
written by nuorain • nuorain
0 votes
0 replies
526 views
Comparison of biodiversity between two locations with a known maximum number of species
shannon ecologie statistics biodiversity
written by y. • y.
1 vote
4 replies
1.5K views
Boxplot with adjustment for variable
r boxplot
updated by zx8754 zx8754 • written by Nona • Nona
1 vote
0 replies
826 views
What is the right choice of normalization and preprocessing before WGCNA using RNAseq data in a cohort?
normalization rna_seq cohort wgcna
written by sukeshinik5 • sukeshinik5
0 votes
5 replies
3.0K views
VCF file generated by Gridss not recognised by VEP
ngs variant-calling vep gridss
updated by Sunnywy0808 • Sunnywy0808 • written by Reda • Reda
0 votes
1 reply
1.1K views
What is more important for Structural Variant Calling? Recall or Precision?
structural-variants merging precision-recall
updated by GenoMax GenoMax • written by Luke • Luke
0 votes
2 replies
1.2K views
Reference genome size for genome size estimation.
genome-size
updated by Ram Ram • written by Shakunthala Natarajan • Shakunthala Natarajan
0 votes
2 replies
1.0K views
Unexpected High T-Base Content in scRNA-seq Fastq Files and GC Bias Correction
fastq fastqc scrna-seq quality-control
written by Cooper • Cooper
2 votes
4 replies
5.5K views
Which Should Take Priority When Selecting DEGs: FDR or Log Fold Change?
deseq2 logfc fdr degs edger
written by bioinfo1994 • bioinfo1994
0 votes
3 replies
1.3K views
batch correction limma package (bead based assay data)
batch-correction
updated by ATpoint ATpoint • written by MC_J • MC_J
0 votes
5 replies
6.7K views
Limma: is it necessary to log-transform the data?
proteomics limma
updated by Gordon Smyth Gordon Smyth • written by eodmacmd • eodmacmd
0 votes
9 replies
2.2K views
I need help with this R script. Thanks.
r
updated by Ram Ram • written by nuorain • nuorain
1 vote
2 replies
1.3K views
Illumina RNA-seq: Overrepresented sequences are mostly in the R2 reads, not R1
illumina rrna rnaseq rna
updated by GenoMax GenoMax • written by Umberto • Umberto
0 votes
3 replies
1.9K views
Using DNA Methylation Data as Input for ChromHMM
chromhmm methylation dna
written by luminea • luminea
0 votes
3 replies
1.4K views
STRUCTURE runs failing: core dumping and slurm exit code 10?
slurm linux structure
updated by GenoMax GenoMax • written by katherinedrotos • katherinedrotos
0 votes
1 reply
821 views
Comparing whole transcriptome under one condition to the transcriptomes under other conditions
transcriptomics
updated by dthorbur dthorbur • written by Texx • Texx
0 votes
0 replies
1.1K views
News: Machine Learning for Multi-Omics Integration (online course) -January 13-15, 2025
machine-learning big-data multi-omics data-integration deep-learning
updated by Ram Ram • written by Physalia-courses Physalia-courses
0 votes
3 replies
1.7K views
How to make DiffBind Run Faster?
diffbind atac-seq
updated by jared.andrews07 jared.andrews07 • written by B.N. • B.N.
0 votes
3 replies
1.3K views
validation approach for CNVs
cnv
updated by WouterDeCoster WouterDeCoster • written by heureuse • heureuse
0 votes
0 replies
764 views
Advisable to perform GSVA on single cells?
gsva scrna-seq
written by bio_info • bio_info
0 votes
0 replies
468 views
Small rna library analysis
sirna small-rna
updated by Ram Ram • written by martta95 • martta95
0 votes
1 reply
825 views
Statistical test to be used for dataset
biostatistics statistical-test
updated by allingt • allingt • written by odi • odi
1 vote
2 replies
1.5K views
Questions Regarding Normalization and Standardization in RNA-seq Differential Analysis
rna-seq normalization
updated by Ram Ram • written by wdasda122 • wdasda122
0 votes
0 replies
666 views
IGV - Load custom variant track
vcf igv react
written by sadapas • sadapas
0 votes
1 reply
1.0K views
Why are the SINEs annotated as zero when using RepeatModeler + RepeatMasker?
sines repeatmodeler repeatmasker
updated by Michael Dondrup Michael Dondrup • written by mut • mut
0 votes
0 replies
650 views
ucsc table browser
ucsc
written by daffodil • daffodil
0 votes
2 replies
1.7K views
Question about various of graph format. How to get the sequence and source of a specific node?
vg
written by chuanj8848 • chuanj8848
0 votes
0 replies
603 views
Facing problems in analysis of bisulfite sequencing data
sequencing bisulfite
updated by GenoMax GenoMax • written by SHREYA • SHREYA
0 votes
2 replies
1.1K views
Can anyone share with me the R code for GSEA analysis?
r code gsea
updated by GenoMax GenoMax • written by nuorain • nuorain
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