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0 votes
3 replies
4.5K views
What software is a good standalone alternative to the Prokka genome annotation software?
annotation-software prokka
updated by GenoMax 16K • | written by bioinformatics_bel 2
1 vote
3 replies
2.7K views
LD SNP pruning with plink
ld-pruning plink
written by celia 1
0 votes
2 replies
933 views
Merging Bismark BED files by loci ?
methylation rrbs transposon bismark
written by anhnguyenbahoang 0
0 votes
2 replies
4.0K views
How to Read .CEL files in R-studio?
r cel affymetrix geo
updated by Ram 4.5K • | written by clara-28 0
0 votes
6 replies
2.0K views
input for gatk VariantAnnotator --dbsnp
variantannotator gatk
updated by GenoMax 16K • | written by QX 9
0 votes
3 replies
1.3K views
Defining the formula/contrasts to detect DEGs between pre vs post treatment
deseq limma
written by Dahham 0
0 votes
5 replies
1.4K views
Normalizacion RNASeq Doubts
normalization bacteria featurecounts rna-seq
updated by Ram 4.5K • | written by Julián 0
0 votes
3 replies
3.1K views
How to Plot Heatmap for Lower Triangular Matrix Using R
r heatmap
updated by Matthias Zepper 524 • | written by ruth 2
0 votes
0 replies
621 views
Squire Pipeline for TE analysis
squire
updated by colindaven 844 • | written by Bioinformatics_16 0
0 votes
5 replies
1.8K views
STAR alignment - high % of reads mapped to multiple loci
star fastqc
updated by Ram 4.5K • | written by sophie 0
0 votes
1 reply
680 views
Transposable detections for long reads
transposable-elements tetyper
updated by GenoMax 16K • | written by Rika 0
0 votes
0 replies
641 views
parseCSQToGRanges in VariantAnnotation
bioconductor
written by ramiro.barrantes 6
0 votes
1 reply
1.1K views
Data Table for MONDO, DOID, UBERON and Cell Ontology
ontology doid cell mondo uberon
updated by Pierre Lindenbaum 17K • | written by Shicheng Guo 963
0 votes
0 replies
680 views
How do I infer the proportion of aneuploid cells using sequencing data?
purecn copynumber next-gen cnvkit wgs
written by Actinidia 0
0 votes
0 replies
586 views
GATK BwaSpark parameter optimisation
parallel-computing gatk bwaspark
updated by Ram 4.5K • | written by Joshua 2
0 votes
4 replies
1.2K views
Doubt regarding Nanomolar calculation for dsDNA
illumina nanomolar
written by alenew.am 1
0 votes
2 replies
1.1K views
how to perform the GSEA for multi groups
gsea
written by alwayshope 4
0 votes
2 replies
1.2K views
kb count -x parameter - what are the three parts?
kb_python umi cell-barcodes kallisto
updated by Assa Yeroslaviz 197 • | written by gogeni5529 9
0 votes
5 replies
1.4K views
Suggestions for resource for running R training
r environments training
updated by Wayne 208 • | written by yura.grabovska 94
0 votes
2 replies
923 views
Small RNA Seq Data-Removing Adapters- Illumina GA2 instrument
sequencing
written by jspe 0
0 votes
1 reply
884 views
computeMatrix on 2 regions with replicates
deeptools chip-seq computematrix
updated by rfran010 174 • | written by asmariyaz23 1
0 votes
0 replies
505 views
Can I use CEMiTool to analyze single cell RNA seq data?
cemitool single-cell
updated by Ram 4.5K • | written by Menna 0
0 votes
2 replies
1.4K views
Filter our reads from multiple hosts
genome metagenome virus host
written by Luca Arbore 1
1 vote
2 replies
911 views
which data type I can use to bulid machine learning.
machine-learning fpkm log2foldchange
written by Qiang 1
0 votes
0 replies
843 views
Accessing PubMed Central full-texts via FTP?
pmcid epmc_ftxt pmc europepmc
written by jeremy.clark 0
0 votes
0 replies
710 views
Navigating Haplotype-Based Association Studies: Software Recommendations and Conversion Challenges
gcta shapeit gwas haplotype phasing
written by PKW 11
0 votes
1 reply
1.2K views
issue with kneaddata
contamination kneaddata
updated by GenoMax 16K • | written by noorehuma 0
0 votes
0 replies
571 views
activepathways background list problem
integration atacseq rnaseq activepathways
written by biology_inform 6
0 votes
2 replies
1.5K views
snpEff database build: FATAL ERROR: No CDS checked
gtf snpeff cds
written by rwherman13 0
0 votes
1 reply
1.8K views
Using Pseudobulk Approach for Identifying Marker Genes Within a Single Condition
differential-expression single-cell pseudobulk
updated by ATpoint 9.1K • | written by nhaus 44
0 votes
2 replies
1.3K views
conda R environment warnings - error
r conda
updated by ATpoint 9.1K • | written by marco.barr 22
0 votes
1 reply
1.3K views
Difference between samtools stats insert size and TLEN in SAM/BAM file.
samtools insert-size sam
updated by Ram 4.5K • | written by krzysm20009042 0
1 vote
11 replies
3.1K views
Can't increase font size for x axis
r ggplot2
written by Chris 36
0 votes
0 replies
735 views
Orientation bias in Mutect2 variant calling
mutect variant-calling
updated by Ram 4.5K • | written by nicola.calonaci 0
0 votes
1 reply
1.2K views
Is it possible to index VCF files and merged the CNVs therein contained using VCF files created from exome sequencing data
variant-calling
updated by Ram 4.5K • | written by yawolberg 1
0 votes
2 replies
985 views
How to find the mapping file for converting Illumina reports SNPid to rsid for build 28 ?
illumina
written by vasank1958 0
1 vote
0 replies
857 views
Predicting ddG stability of multi-mutation protein variants
ddg protein-stability
updated by Ram 4.5K • | written by liorglic 150
0 votes
4 replies
1.3K views
Make the normalized counts from treatment relative to control-EdgeR
normalized-counts edger
updated by Ram 4.5K • | written by Pamela 0
1 vote
2 replies
1.6K views
How to Specify genome version (GRCh37 release 104) in VEP REST API?
vep
updated by Ram 4.5K • | written by gcampof 2
0 votes
4 replies
1.7K views
Missense variant proteins 3D Structure prediction
model protein-structure alphafold
written by Esraa 1
0 votes
2 replies
860 views
Can I analyze single-end and paired-end RNA-Seq data together?
rna-seq
updated by pinheirofabiano 14 • | written by roxana 1
0 votes
1 reply
717 views
T cell subtype annotation
seurat single-cell singlecellexperiment
updated by allingt 4 • | written by georgii.vdovin 0
0 votes
0 replies
666 views
Job: PhD positions for autoimmune disease at UKSH/Uni Luebeck
phd autoimmune-disease
updated by Ram 4.5K • | written by alwayshope 4
1 vote
14 replies
3.5K views
vg installation on MacOS failing: "ld: -headerpad: not a hexadecimal number: -headerpad_max_install_names"
macos vg
updated by GenoMax 16K • | written by Nathan 1
0 votes
6 replies
3.0K views
SPADES Result Comparison
illumina genome spades assembly
written by SomeOne 33
0 votes
0 replies
682 views
How to Obtain a GMT File for Pathway Enrichment Analysis in Gallus gallus Metabolomics Data?
metabolomics gsea pathways gmt
written by DareDevil 448
0 votes
0 replies
675 views
mismatch allele problem PLINK
plink
updated by Ram 4.5K • | written by luca.sclisizzo 0
0 votes
0 replies
611 views
RepeatMasker. Repeat identification.
repeatmasker
written by Николай 0
0 votes
0 replies
726 views
News: Online course: Metabolomics with R/Bioconductor (5th edition)
metabolomics bioconductor r
updated by Ram 4.5K • | written by Physalia-courses 281
0 votes
1 reply
985 views
I am getting an error with Kallisto Bustools wrapper (kb) command to create an index
kb kallisto bustools
updated by dsull 781 • | written by biotrekker 11
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