This is a test version of Biostars. For the public version, visit https://www.biostars.org.
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0 replies
648 views
Example - Meta Analysis TCGA and DepMap
meta-analysis tcga depmap
updated by Ram Ram • written by joseph.landry • joseph.landry
0 votes
4 replies
1.3K views
bcftools select sites with multiple combinations of FILTER column
bcftools
written by User000 User000
0 votes
1 reply
914 views
Extract Umi sequence to readname
sequence fgbio umi
updated by GenoMax GenoMax • written by Smilesky • Smilesky
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3 replies
2.5K views
Combining and Forward and Reverse Reads
genome alignment concatenation sequencing
written by SineWave • SineWave
0 votes
1 reply
2.6K views
Genbank Bacteriophage Genome Submission - Internal stop codons in CDS sequences
cds genome ncbi genbank
updated by Ram Ram • written by Sowmya Pulapet • Sowmya Pulapet
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0 replies
1.6K views
Blog: WGBS vs RRBS
rrbs dna-methylation wgbs
updated by Ram Ram • written by Novogene • Novogene
0 votes
6 replies
1.7K views
Quest about the input data for PCA analysis
pca
written by tujuchuanli tujuchuanli
0 votes
2 replies
1.1K views
How to visualize scRNA-seq normalized data
seurat 10x scrna-seq single-cell normalization
written by SlowSD • SlowSD
0 votes
1 reply
837 views
Disease Prevalence Database/Disease Incidence Database
prevalence
updated by Ram Ram • written by Shicheng Guo Shicheng Guo
0 votes
6 replies
2.3K views
Need consultation about my rna-seq workflow
rna-seq gene-expression
updated by Ram Ram • written by markusz • markusz
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7 replies
4.0K views
cutadapt not trimming all adapters in PE Illumina sequencing
ngs illumina cutadapt
written by noodle noodle
0 votes
1 reply
949 views
Using multiple reference genomes for alignment in dorado?
dorado basecall ont alignment
updated by GenoMax GenoMax • written by gideonav • gideonav
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1 reply
899 views
Automatic protein symmetry classification from PDB coordinates
pdb symmetry protein
updated by Mensur Dlakic Mensur Dlakic • written by Kartik • Kartik
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7 replies
2.6K views
'Invalid parameter' error to generate a count matrix using featurecounts
rna-seq featurecounts
updated by GenoMax GenoMax • written by Shay • Shay
0 votes
1 reply
1.0K views
Find out shared differentially expressed genes between two cell lines due to knockdown treatment
differential-gene-expression rna-seq
updated by Ram Ram • written by Xinqi • Xinqi
1 vote
16 replies
7.3K views
visualize CNV data based on WGS
cnv
updated by clealk • clealk • written by Bogdan Bogdan
0 votes
1 reply
785 views
Seeking for edgeR TMM Normalization calcul example
tmm edger deseq2
updated by jared.andrews07 jared.andrews07 • written by Picasa Picasa
0 votes
0 replies
782 views
Tool: MicrobiomePhylo: A Comprehensive Platform for Advanced Microbiome Amplicon Sequencing Data Analysis and Visualization
microbiome analysis data 16s
written by camillatafuro • camillatafuro
0 votes
0 replies
533 views
Tool for power calculation in GWAS for quantative trait
trait quantative power calculation gwas
written by chevivien chevivien
0 votes
1 reply
1.3K views
Advice for genetic diversity stats analysis with both variant and variant sites
pi diversity vcf genetics
updated by dthorbur dthorbur • written by ekirsch • ekirsch
0 votes
1 reply
713 views
How to find and visualize expression level of a dataset?
r
updated by BioinfGuru BioinfGuru • written by uveyik • uveyik
0 votes
3 replies
1.4K views
How to validate the assembly completeness of unaligned reads ?
masurca spades
updated by GenoMax GenoMax • written by Sony Nguyen • Sony Nguyen
0 votes
3 replies
1.9K views
Maximum returned records using epost?
e-utilities biopython
updated by GenoMax GenoMax • written by theclubstyle • theclubstyle
0 votes
1 reply
798 views
PEAR seems to have sense to me
pear
updated by GenoMax GenoMax • written by ManuelDB ManuelDB
0 votes
1 reply
811 views
Interprete plot of dispersion estimation by DESeq2
dispersion dexseq deseq2
updated by Pierre Lindenbaum Pierre Lindenbaum • written by tien • tien
0 votes
3 replies
1.6K views
Annotate genes from gtf file to vcf file
gtf genomics vcf
written by QX • QX
1 vote
3 replies
1.2K views
Read length distribution of whole genome sequnces of human
fastq read fastqc
written by Yellapu • Yellapu
0 votes
1 reply
726 views
Adding gene to GRange objects with single base
granges genomics
updated by ATpoint ATpoint • written by QX • QX
0 votes
2 replies
1.0K views
Infering the cell composition from bulk RNA-seq data for mouse
rna-seq deconvolution mouse
written by feather-W • feather-W
0 votes
2 replies
1.1K views
Gene set to perform GSVA
gsva
written by CTLong • CTLong
1 vote
5 replies
1.5K views
How to find gene ids for Pfam ids?
pfam gene
written by WUSCHEL WUSCHEL
0 votes
4 replies
1.6K views
Pearson correlation between Gene and clinical parameters
read-counts pearson-correlation
updated by Shred Shred • written by Mary • Mary
0 votes
1 reply
888 views
Capped expression values in single cell RNAseq (Tabula Sapiens/scanpy/CellXGene)
scanpy cellxgene scrna-seq 10x normalisation
written by matt.a.bennett25890 • matt.a.bennett25890
0 votes
1 reply
1.1K views
RNA-seq scaling the data for heatmap
rna-seq heatmap scaling
updated by matt.a.bennett25890 • matt.a.bennett25890 • written by maplewj • maplewj
0 votes
11 replies
2.2K views
bedToBigBed error, what am I doing wrong?
homer software-error ucsc
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Ronin • Ronin
1 vote
2 replies
2.4K views
R: How to customize the legend order for a 3D scatter plot in plotly?
r r plotly
written by SIV0625TriX • SIV0625TriX
0 votes
3 replies
5.4K views
Single cluster spanning in different locations in UMAP in scRNAseq data
umap scrnaseq
written by sarahmanderni sarahmanderni
0 votes
4 replies
1.4K views
Biostrings extract read
r fastq biostrings
written by marco.barr • marco.barr
0 votes
2 replies
1.2K views
Detecting viruses in human rna seq data
rna-seq viruses
updated by GenoMax GenoMax • written by biochugs • biochugs
0 votes
0 replies
617 views
Change orig.ident column in seurat meta.data to match cell barcode sample prefixes
seurat
written by bgbs • bgbs
0 votes
2 replies
1.1K views
Length by gene from salmon
salmon rna-seq
written by marco.barr • marco.barr
0 votes
4 replies
2.6K views
change order of violin plots in ggplot2
r ggplot2 violin-plots
updated by Ram Ram • written by Matteo Ungaro • Matteo Ungaro
0 votes
0 replies
676 views
Motif analysis by HOMER
homer
written by daffodil • daffodil
0 votes
2 replies
1.8K views
Applicability of the SoupX ambient mRNA decontamination technique to fixed and/or multiplexed scRNAseq experiments
soupx scrna-seq
written by e.r.zakiev • e.r.zakiev
0 votes
5 replies
2.4K views
Error when trying to install R package 'scater'
scater scrna-seq
updated by Ram Ram • written by Nitin • Nitin
0 votes
4 replies
2.4K views
Long branch lengths, low bootstrap values and misalignments
mafft muscle iqtree
written by samyu.senthil • samyu.senthil
2 votes
5 replies
2.1K views
Including reference genome in SNP-based phylogeny
phylogeny vcf wgs
written by maxrwjones • maxrwjones
1 vote
5 replies
1.4K views
How to add FORMAT/TAG = "." to all samples in a vcf file via bcftools?
vcf bcftools
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Марта • Марта
0 votes
1 reply
962 views
adding new assemblies to previously built practical haplotype graph (v2)
pangenome phg_v2 plants phg
updated by lcj34 lcj34 • written by b.contreras.moreira • b.contreras.moreira
0 votes
2 replies
1.4K views
Ribo and RNA seq analysis
rna-seq genomics ribo-seq
updated by Jack Tierney • Jack Tierney • written by Manu Ayllon • Manu Ayllon
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