This is a test version of Biostars. For the public version, visit https://www.biostars.org.
0 votes
6 replies
1.4K views
Comparability between normalized Counts / TPMs and log2FoldChange
foldchange tpms deseq2 normalized rnaseq counts
written by NorbertK • NorbertK
0 votes
1 reply
775 views
Assistance Required: Error with MuSiC2 Package - "pVar" Function Not Found
music2
updated by Bastien Hervé Bastien Hervé • written by Pumla • Pumla
1 vote
2 replies
1.8K views
Forum: Do you agree with the practice of combing TCGA with GTEx?
gtex tcga
updated by i.sudbery i.sudbery • written by nuorain • nuorain
0 votes
7 replies
3.4K views
Help with Funannotate
genomes funannotate fungus annotation
updated by lieven.sterck lieven.sterck • written by SomeOne • SomeOne
0 votes
2 replies
796 views
Annotations Tools
annotations for tools
written by abebe1423 • abebe1423
0 votes
3 replies
1.1K views
Alphafold in colab - homotrimer
homotrimer
updated by dthorbur dthorbur • written by sjp24 • sjp24
0 votes
0 replies
572 views
Different results with 'clara-parabricks fq2bam' and bowtie2
fq2bam clara-parabricks fastq bowtie2
written by Lars • Lars
0 votes
0 replies
556 views
GWAS to gene function prediction
annotation vcf gwas prediction gene
written by alnus • alnus
2 votes
2 replies
993 views
miRNAs - Adapters, adapters, adapters i´m so confused
mirna-seq geo adpaters mirnas
updated by Ram Ram • written by omicon • omicon
0 votes
2 replies
830 views
DEseq2: Advice for model (double interaction ?)
deseq2 matrix dge
written by Picasa Picasa
0 votes
1 reply
884 views
Kallisto alignment with HPC (SLURM)
slurm hpc kallisto alignment
updated by dsull dsull • written by tekica • tekica
0 votes
0 replies
426 views
KEGG pathways
kegg pathways
written by Blue • Blue
0 votes
4 replies
1.4K views
Protein-Protein Network
cytoscape genes breast-cancer network
updated by Ram Ram • written by abdullah • abdullah
0 votes
5 replies
2.8K views
Correct format for Hi-C matrix before converting to BEDPE
juicer matrix bedpe hi-c
updated by kalavattam • kalavattam • written by desptsp • desptsp
0 votes
0 replies
634 views
News: Mass Spectrometry and Proteomics using R and Bioconductor course
r bioconductor mass-spectrometry proteomics
updated by Ram Ram • written by Physalia-courses Physalia-courses
0 votes
0 replies
598 views
How to download data from MGRAST
mgrast microbiome metagenome
written by Maxwell • Maxwell
0 votes
2 replies
967 views
Gene level expression versus variant-level expression
variant rnaseq
written by ramiro.barrantes • ramiro.barrantes
0 votes
1 reply
907 views
Java error in BEAST2
beast2 java
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Rafae • Rafae
0 votes
10 replies
6.0K views
Bedmethyl file format
bedmethyl methylation
updated by lavigne • lavigne • written by njornet • njornet
0 votes
4 replies
1.5K views
Tool: PIASO, a python toolkit for single-cell data analysis
data-integration scrna-seq normalization scatac-seq spatial-transcriptomics
written by Min • Min
2 votes
6 replies
4.8K views
Forum: What is the current state of the beef against UMAP/tSNE in the context of sc trajectory analysis/monocle3?
monocle3 umap single-cell tsne trajectory
written by txema.heredia • txema.heredia
1 vote
1 reply
1.0K views
Type of Pangenome Type/program to use for fungal isolates of the same species, but have major translocations
visualization pangenome genome alignment
updated by samuel.a.odonnell samuel.a.odonnell • written by Drew • Drew
0 votes
0 replies
474 views
Finding Indel Mutant structures
indel
written by Logan • Logan
0 votes
0 replies
800 views
Doublet Detection for Intestinal Immune Cells in scRNA-seq
scdblfinder seurat scrna-seq doublets immune
written by s • s
0 votes
7 replies
4.0K views
Compare genomes of different species and published studies (different years, sequencing technologies...) is correct?
comparative-genomics
updated by SanjidaR_NCBI • SanjidaR_NCBI • written by Bruno Santos • Bruno Santos
0 votes
1 reply
957 views
no "-" strand in transcriptome alignment
drs transcriptome alignment
updated by GenoMax GenoMax • written by baibhu1234 • baibhu1234
0 votes
3 replies
2.4K views
What is best way to do CNV Analysis on Xenium data (Spatial transcriptomics)?
seurat xenium spatialtranscriptomics singlecell
updated by yura.grabovska • yura.grabovska • written by geno89 • geno89
0 votes
3 replies
1.2K views
Finding a gene in human
variant gene
updated by Ram Ram • written by zizigolu zizigolu
0 votes
4 replies
1.9K views
Assigning cell annotation based on calculated scores.
clustering seurat ucell cell-annotations score
updated by ATpoint ATpoint • written by Assa Yeroslaviz Assa Yeroslaviz
0 votes
0 replies
537 views
single cell rna seq NMF Error in which.min(sapply(res.runs, "[[", "residuals"))
error sc-rna-seq seurat nmf
updated by Bastien Hervé Bastien Hervé • written by Beatriz • Beatriz
0 votes
1 reply
899 views
Low quality of NGS SNP analysis panel
fastqc iontorrent ngs
updated by Prash • Prash • written by kate-nelis • kate-nelis
0 votes
4 replies
1.5K views
Multiple fail points in fastqc file
fastqc report
written by dr.deepakkukkar • dr.deepakkukkar
0 votes
1 reply
945 views
mapping to transcriptome.fasta vs genome.fasta
mapping gtf transcriptome genome
updated by Mensur Dlakic Mensur Dlakic • written by baibhu1234 • baibhu1234
0 votes
2 replies
924 views
Where to find WGS, metagenome data for obesity group?
hmp microbiome data ncbi metagenomics
updated by ehaag • ehaag • written by Emily • Emily
0 votes
2 replies
927 views
WDL 1.0 - Directory Type
directory input wdl
written by davidmaimoun • davidmaimoun
0 votes
1 reply
823 views
How to input INDELs in ped files
snp r haplostats haploview indel
updated by Mwangana • Mwangana • written by Ant • Ant
1 vote
0 replies
675 views
Tool: HGVSV: A tool to parse and generate HGVS names with Structural Variant support
variants hgvsv variant hgvs structural
written by parker.payne • parker.payne
0 votes
3 replies
1.5K views
P-value calculation between groups in split violin plot
violinplot ggplot singlecellrnaseq
updated by LChart LChart • written by AB AB
0 votes
3 replies
2.4K views
After doublet detection in 10x scRNA-Seq data, there is still evidence of doublets
r doubletfinder seurat scrna
written by yura.grabovska • yura.grabovska
0 votes
0 replies
596 views
Hash-Based Allele Calling
calling hash allele
written by davidmaimoun • davidmaimoun
0 votes
0 replies
488 views
Issues with FPKM Calculation in RNA-seq Analysis (Apodemus agrarius)
fpkm. cufflinks
updated by lieven.sterck lieven.sterck • written by ohtang7 • ohtang7
1 vote
5 replies
1.6K views
Metagenomics/amplicon sequencing: Most publicly available data already host removed sequences or no?
amplicon decontamination qc microbiome metagenomics
written by Maxwell • Maxwell
0 votes
1 reply
973 views
plot PLINK2.0 output with ggtree
ibs matrix plink ggtree
written by Matteo Ungaro • Matteo Ungaro
0 votes
3 replies
1.0K views
PCA for Batch effect
batch wes pca effect
updated by mark.ziemann mark.ziemann • written by SIMONE • SIMONE
0 votes
3 replies
1.0K views
Looking for an old-fashioned alignment editor
msa editor
updated by GenoMax GenoMax • written by Suicyte • Suicyte
0 votes
0 replies
584 views
eQTL mapping with imputed genotypes: use data from GT or DS slot of VCF?
eqtl vcf imputation matrixeqtl
written by Colari19 Colari19
0 votes
1 reply
763 views
Query on WES
wes
updated by Ram Ram • written by rauf.sania786 • rauf.sania786
0 votes
0 replies
666 views
Replace heterozygous genotypes with minor allele in a vcf file
genotype snp vcf heterozygous
written by kumar.vinod81 kumar.vinod81
1 vote
4 replies
1.2K views
Enrichment analyses (GO TERM etc)
clusteprofiler somascan proteins enrichment
updated by mark.ziemann mark.ziemann • written by kl • kl
0 votes
2 replies
804 views
Protoplast Transient Assay in Arabidposis
transient-assay protoplast arabidposis
updated by dthorbur dthorbur • written by Maryam • Maryam
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