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0 votes
1 reply
615 views
Questions about sample_accession_id and file_accession_id from EGA files
ega open wgs data
updated by GenoMax GenoMax • written by askif4 • askif4
0 votes
1 reply
680 views
Functional Analysis Using EMU Output – Has Anyone Tried This?
emu
updated by andres.firrincieli andres.firrincieli • written by henrique.mouradias • henrique.mouradias
0 votes
3 replies
953 views
featureCounts -t option not working in v2.0.8?
subread featurecounts rnaseq
updated by rfran010 • rfran010 • written by atan • atan
0 votes
1 reply
927 views
mm10 blacklist regions detailed information
sequencing dna blacklist
updated by GenoMax GenoMax • written by annaA • annaA
0 votes
2 replies
803 views
identify unmapped regions
human illumina libraries
written by María José • María José
0 votes
1 reply
865 views
martCheck - Error - You must provide a valid Mart object - for running HoneyBADGER for CNV computation
cnv biomart honeybadger
written by mete.han.celebi • mete.han.celebi
0 votes
1 reply
813 views
How to Specify Power Parameter for Adjacency in modulePreservation() (WGCNA)
module analysis wgcna preservation
updated by andres.firrincieli andres.firrincieli • written by Berkan • Berkan
0 votes
1 reply
666 views
filters used in mutation discovery from RNAseq data
filter rnaseq mutation
updated by GenoMax GenoMax • written by htchd • htchd
0 votes
6 replies
1.4K views
Trouble Using GEO Files with Seurat
seurat geo scrna
updated by antonioggsousa antonioggsousa • written by Jamie • Jamie
0 votes
0 replies
727 views
Knowledge Graph for AI
knowledgegraph biotech ai spoke bioinformatician
written by Cornelio • Cornelio
0 votes
2 replies
1.3K views
How to convert from .spec to .bam?
bam file-formatting spec
updated by Daniel Lai • Daniel Lai • written by gmora • gmora
0 votes
1 reply
863 views
Insert size is zero
rna-seq fastp insert size
updated by GenoMax GenoMax • written by SpliceAndScript • SpliceAndScript
0 votes
3 replies
1.3K views
Should matched samples (not paired) be included in the DESeq2 design model?
edger limma deseq2
updated by i.sudbery i.sudbery • written by marieke • marieke
0 votes
4 replies
1.4K views
Trajectory Analysis scRNA-seq with one cell type and two developmental stages
cellrank palantir pseudotime-trajectory-analysis scrna-seq trajectory-analysis
written by npont • npont
0 votes
1 reply
960 views
How to run trajectory analysis with only one cell type using palantir?
palantir scanpy
updated by npont • npont • written by bioinfo • bioinfo
0 votes
1 reply
657 views
should I remove the transcripts from annotate peak region in ATAC-seq
atac-seq
updated by rfran010 • rfran010 • written by QX • QX
1 vote
2 replies
1.3K views
DESeq2 LRT test with multifactorial design
test design multifactorial lrt
written by lessismore lessismore
1 vote
0 replies
1.6K views
Tool: Created a better alternative to clunky gene databases, with functions that are consolidated from various gene databases. It's your one-stop shop for gene info!
browser export data search gene
written by Krish • Krish
1 vote
0 replies
620 views
Tool: Containerized NGS Data Processing Pipelines
rna-seq atac-seq pipeline chip-seq docker
written by Noah • Noah
0 votes
0 replies
568 views
Genotype Imputations Question
vcf imputations genomics
written by Jonathan • Jonathan
0 votes
1 reply
787 views
Clarification of options --keep-dup: all vs. -f FRAG in MACS3
human libraries illumina callpeak macs3
updated by ATpoint ATpoint • written by María José • María José
3 votes
4 replies
1.4K views
Should I perform integration to correct batch effects?
batch effect
updated by antonioggsousa antonioggsousa • written by han • han
0 votes
1 reply
704 views
Batch correction in TNBC epithelial cells
tnbc seurat epithelialcells scrnaseq batcheffect
updated by ATpoint ATpoint • written by TNF_alpha • TNF_alpha
1 vote
5 replies
2.2K views
Best way to install R packages on an HPC?
r hpc
updated by Charles Plessy Charles Plessy • written by ChumBucket2024 • ChumBucket2024
2 votes
2 replies
864 views
how to use filter_vep to filter vcf file
vcf filter
written by htchd • htchd
0 votes
2 replies
953 views
How to interpret genomescope to help remove duplicates
assembly hifi genomescope
written by mohamadelian1996 • mohamadelian1996
0 votes
2 replies
725 views
Is it valid to stack brightfield and fluorescence channels in a CNN input?
fluorescent-microscopy imaging microscopy
updated by LChart LChart • written by Antonio • Antonio
0 votes
0 replies
423 views
FusionCatcher cases where gene1 and gene 2 have 2 matches
fusions fusioncatcher
written by ieie • ieie
0 votes
2 replies
803 views
mgl tool index error
docking molecular error
written by Mahesh • Mahesh
0 votes
3 replies
1.1K views
convert raw counts to TPM
r
updated by dthorbur dthorbur • written by pinheirofabiano • pinheirofabiano
0 votes
7 replies
2.6K views
Creating kraken2 custom database
kraken2
updated by GenoMax GenoMax • written by ramiro.barrantes • ramiro.barrantes
0 votes
0 replies
570 views
How to determine the coordinate of the transposon insertion on the reverse reading?
tn-seq transposon blastn
written by Елизавета • Елизавета
0 votes
8 replies
2.0K views
Single-cell RNA Sequencing - transcript abundance estimation using Alevin-Fry
alevin-fry single-cell sequencing salmon rna
updated by GenoMax GenoMax • written by wooh • wooh
0 votes
0 replies
796 views
News: Conservation Genomics course
populationgenomics ne conservationgenomics
written by Physalia-courses Physalia-courses
0 votes
3 replies
941 views
Snakemake Module Error: string indices must be integers
gatk snakemake
updated by Jesse • Jesse • written by andean • andean
0 votes
3 replies
855 views
How do I generate a Manhattan plot like this?
data-visualization manhattan-plot
written by mert • mert
0 votes
2 replies
980 views
ATAC seq: from peaks to differential analysis ??
macs2 deseq2 atacseq
updated by rfran010 • rfran010 • written by Picasa Picasa
0 votes
1 reply
690 views
Where to find expected copy number for a gene
genomics
updated by GenoMax GenoMax • written by LayneSadler LayneSadler
0 votes
4 replies
2.0K views
Cut&Run replicates handling
peakcaller replicates seacr chipseq
updated by schowdhury8950 • schowdhury8950 • written by g.anande • g.anande
0 votes
1 reply
1.1K views
Unable to extract count matrices from multi-layered Seurat object
seurat
written by bgbs • bgbs
3 votes
12 replies
2.6K views
Learning Nextflow
genomic pipeline_analysis nextflow
written by AIMAR • AIMAR
1 vote
1 reply
796 views
open target platform SNP to Gene qurey
snptogene gwas snp
updated by GenoMax GenoMax • written by SeoG • SeoG
0 votes
1 reply
880 views
usage of ChromHMM and Segway
chromhmm segway
updated by Pierre Lindenbaum Pierre Lindenbaum • written by qian • qian
1 vote
6 replies
2.8K views
Which tools do you recommend me use to get the maximum information of a protein?
protein software
updated by fileyfood • fileyfood • written by Hamtaro • Hamtaro
3 votes
4 replies
2.5K views
Tools for predicting protein function?
protein
updated by fileyfood • fileyfood • written by jamie.pike jamie.pike
3 votes
12 replies
4.8K views
Map genome positions onto protein coordinates?
pdb protein variant
updated by fileyfood • fileyfood • written by cmdcolin cmdcolin
3 votes
3 replies
2.1K views
Online tool for creating figures of gene with its features
features genes figures
updated by fileyfood • fileyfood • written by andre.arrudalima • andre.arrudalima
1 vote
7 replies
2.3K views
Simple tools for creation of figures of gene and protein structure
gene protein
updated by Krish • Krish • written by andre.arrudalima • andre.arrudalima
2 votes
3 replies
1.9K views
To create amino acid substitution in protein structure
protein software
updated by fileyfood • fileyfood • written by shwetamgr1 • shwetamgr1
6 votes
13 replies
14K views
Where Can I Get The Secondary Structure Of A Protein?
protein structure sequence
updated by Krish • Krish • written by Giovanni M Dall'Olio Giovanni M Dall'Olio
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