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maftools oncoplot top bar barplots - any way to customize this plot further with color aesthetics or cutoff lines?
maf maftools oncoplot exome
updated 15 months ago by 45k • written 15 months ago by ▴ 10
0
votes
4
replies
831
views
Help with CNA analysis using control-FREEC
CNA control-FREEC
15 months ago by sainavyav22 • 0
1
vote
2
replies
797
views
Access to Giraffe sequence data
nature giraffe data-access
updated 15 months ago by 45k • written 15 months ago by ▴ 80
0
votes
1
reply
480
views
Best kit for PacBio HiFi Sequencing preperation
PacBio-sequencing PacBio-HiFI HMW-gDNA
updated 15 months ago by 45k • written 15 months ago by • 0
1
vote
1
reply
799
views
Diffbind fold values and parameter Fold in DBA.report function
DESEQ2 ATAC-seq DBA.report Diffbind
15 months ago by Manko47 ▴ 10
0
votes
2
replies
742
views
Conservation scores at each location of few motifs in MSA
conservation-scores FASTA MSA
14 months ago by wannabio • 0
0
votes
1
reply
689
views
How lambda parameter works in BLAST?
lambda BLAST
updated 15 months ago by ★ 1.3k • written 15 months ago by • 0
6
votes
3
replies
1.8k
views
GSEA with fgsea package and using stat from DESeq2 output - what to do with NA padj values?
RNA-seq DESeq2 GSEA
15 months ago by Fossil ▴ 30
0
votes
1
reply
798
views
Editing seurat object metatdata
Seurat metadata scRNA-seq
updated 15 months ago by ▴ 100 • written 15 months ago by • 0
6
votes
1
reply
1.4k
views
Tutorial: How to organize a computational biology project
file-organization
updated 15 months ago by ★ 30k • written 15 months ago by ★ 4.7k
1
vote
1
reply
753
views
Why the UK biobank switch off the data download facilities?
UKB
updated 15 months ago by • 0 • written 15 months ago by ▴ 10
0
votes
2
replies
872
views
How to download BLCA.focal_score_by_genes.txt from GDC
GDC
updated 15 months ago by ★ 1.3k • written 15 months ago by • 0
6
votes
3
replies
1.0k
views
Maximum bits in ggseqlogo is less then 2?
ggseqlogo
updated 15 months ago by ★ 3.1k • written 15 months ago by ▴ 10
2
votes
4
replies
1.1k
views
Construction of a phylogentic tree for thousands of bacterial genomes
Phylogenomics
updated 15 months ago by ★ 30k • written 15 months ago by ▴ 150
0
votes
2
replies
662
views
Adding a simple tag to VCF Info column
vcf
updated 15 months ago by 45k • written 15 months ago by ▴ 30
1
vote
1
reply
736
views
Automated methods for comparing trees
distance agglomerative compare tree
updated 15 months ago by ★ 30k • written 15 months ago by 36k
1
vote
3
replies
772
views
Pdb file isn't opening in the Desmond
Simulation MD
15 months ago by 20212854117sakib • 0
0
votes
4
replies
1.1k
views
Bulk converting superseded TCGA UUIDs
R TCGAutils TCGA
updated 15 months ago by ★ 1.3k • written 15 months ago by ▴ 90
0
votes
1
reply
523
views
Are bam2fastq --no-aligned and samtools fastq -f 4 same?
samtools assembly spades fastq
updated 15 months ago by 166k • written 15 months ago by • 0
3
votes
2
replies
2.1k
views
Seurat object with multiple PCAs/UMAPs from different assays
R Seurat
updated 15 months ago by ★ 3.1k • written 15 months ago by • 0
0
votes
2
replies
827
views
How to find column names for ENCODE ATAC-seq data?
encode atac-seq bed
updated 15 months ago by ★ 4.7k • written 15 months ago by ▴ 20
0
votes
2
replies
1.4k
views
miRNAs pathway analysis
pathway miRNA
updated 15 months ago by • 0 • written 4.0 years ago by ★ 4.4k
7
votes
0
replies
574
views
Tool: GeneScape: A Python package for gene ontology visualization
ontology GO
15 months ago by Istvan Albert 103k
3
votes
0
replies
24k
views
Herald: The Biostar Herald for Monday, June 10, 2024
herald
15 months ago by Biostar 3.6k
0
votes
1
reply
677
views
Automated my docking results by using script
Receptor-ligand-interaction DSV VINA
updated 15 months ago by 45k • written 15 months ago by • 0
0
votes
4
replies
1.1k
views
gene expression design
R gene-expression RNA-seq
15 months ago by bioinfo1994 ▴ 20
3
votes
4
replies
1.2k
views
QC Analysis from Sanger sequencing
qc ab1 sanger
15 months ago by davidmaimoun ▴ 50
1
vote
1
reply
768
views
How to calculate the Genetic Distance (P-Distance) by using mtDNA pacBio data?
pacBio Genetic-Distance mtDNA
15 months ago by hashim.rana11 ▴ 40
2
votes
3
replies
1.1k
views
bash for merging bam files by samtools
samtools
updated 15 months ago by 154k • written 15 months ago by ▴ 80
0
votes
1
reply
749
views
Extremely high variance of coverage for metagenomic sample (variance-to-mean ratio ~2.5)
MetaBAT metagenome coverage
15 months ago by k-tarasov • 0
0
votes
2
replies
3.5k
views
blastn_vdb "- Error opening the following db(s): "
sra sra-toolkit blast blastn_vdb wgs
updated 15 months ago by • 0 • written 8.7 years ago by ▴ 30
1
vote
0
replies
1.0k
views
Tutorial: SingleCellExperiment object explained with a real-world example
bioconductor scRNA-seq single-cell
updated 15 months ago by 45k • written 15 months ago by ★ 4.7k
2
votes
2
replies
1.2k
views
deeptools Compute reference-point and scale-regions
deeptools computeMatrix plotprofile
15 months ago by RD ▴ 30
0
votes
3
replies
1.2k
views
Clusters in Differential Gene Expression Data
gdc gene-expression seurat
updated 15 months ago by ★ 1.3k • written 16 months ago by • 0
0
votes
1
reply
629
views
Exon count and GC content
Exon-count GC-content
updated 15 months ago by 166k • written 15 months ago by • 0
3
votes
4
replies
1.3k
views
Making heatmaps of ATACseq annotation data in R?
ATAC-seq RStudio
updated 15 months ago by ★ 1.6k • written 15 months ago by ▴ 10
2
votes
2
replies
766
views
What does the name of a read mean? How to find its location in genome viewer?
ukb reads
updated 15 months ago by 166k • written 15 months ago by • 0
0
votes
3
replies
1.1k
views
Detecting a virus in RNA-Seq Data
fastq-screen Rna-seq kraken2
updated 15 months ago by ★ 1.6k • written 15 months ago by ▴ 20
1
vote
2
replies
823
views
finding housekeeping genes and small RNA sequences of Arabidopsis thaliana
housekeeping-genes RNA
15 months ago by analyst ▴ 70
2
votes
2
replies
857
views
getting RNA-seq raw counts from Kallisto
counts raw RNA-seq Kallisto
15 months ago by Meghan.T ▴ 10
0
votes
1
reply
782
views
What database to use for GATK baseRecalibration when using the ensembl hg19 genome
ensembl gatk
updated 15 months ago by 154k • written 15 months ago by ▴ 60
0
votes
1
reply
737
views
Design model matrix with limma with cell different proportions estimates and batch effect
R limma deconvolution RNA-Seq
updated 15 months ago by ★ 8.3k • written 15 months ago by • 0
0
votes
1
reply
531
views
Looking for a scientific source talking about the functionality of CONCOCT and MetaBAT
sources CONCOCT assembly METABAT
updated 15 months ago by ▴ 60 • written 15 months ago by ▴ 10
0
votes
19
replies
2.9k
views
Rstudio hangs on logisic regression using generalized estimating equations (geepack::geese())
geepack
15 months ago by jonas.andersson ▴ 40
0
votes
6
replies
1.7k
views
Network analysis of TCGA and GTEx gene expression datasets
R GTEx studio TCGA
updated 15 months ago by ▴ 180 • written 15 months ago by • 0
4
votes
7
replies
1.4k
views
fastq-dump not working in loop
fastq-dump
updated 15 months ago by 45k • written 15 months ago by ▴ 70
3
votes
5
replies
1.2k
views
assemble extracted kmers into longer contigs/sequences
assembly unique kmers
15 months ago by sapuizait ▴ 10
3
votes
4
replies
1.4k
views
Error: Trimmomatic Command not found
NGS Illumina Quality-Control Trimmomatic
updated 15 months ago by 45k • written 15 months ago by ▴ 10
1
vote
2
replies
831
views
single nucleus RNA seq processing pipeline questions
demultiplexing snRNAseq
14 months ago by biotrekker ▴ 110
0
votes
0
replies
482
views
Add gene expression boxplot from plotCounts to each row of oncoprint via ComplexHeatmap
R ComplexHeatmap oncoprint
updated 15 months ago by 45k • written 15 months ago by ▴ 230
121,931 results • Page 101 of 2439
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Answer: allele frequency in VCF
Understanding terms, specifically relating to GT:PL in a VCF file
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Answer: Does this adapter content from fastqc to warrant trimming prior to alignment?
Answer: Does this adapter content from fastqc to warrant trimming prior to alignment?
Looking to learn practical bioinformatics
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Comment: What happened to biomart.org by Jeremy Leipzig 23k
same with geuvadis.org
Comment: real time PCR data analysis by Gordon Smyth ★ 8.3k
Are you doing qPCR for one gene or for several genes?
Comment: protein interaction prediction by Fatemeh ▴ 50
Thanks very much for your help. I need to try it.
Comment: real time PCR data analysis by Fatemeh ▴ 50
Thanks a lot for the link. The problem is that with this repeated measures, if you put the data from different donors in different rows, fo…
Answer: What happened to biomart.org by GenoMax 154k
Looks like EBI let the domain registration expire. The domain was picked up by someone else and turned into the site OP mentions. There use…
Comment: Hifiasm is getting killed while trying to assemble a genome by GenoMax 154k
> I want to reconstruct the assembly using the pacbio reads only. Is there a paper associated with this data? If the original publication/…
Comment: real time PCR data analysis by ATpoint 89k
I think the keyword to go after here is repeated measures https://www.graphpad.com/guides/prism/latest/statistics/repeated_measures.htm
Answer: What happened to biomart.org by ATpoint 89k
Maybe I am missing sth because I've never used the website but only the API and R interface, but I think the website has always been https:…
Comment: protein interaction prediction by Fatemeh ▴ 50
It is most probably binding to a protein. Its function is somehow known though, which is good . Thanks very much for the link. I will have …
Comment: Looking to learn practical bioinformatics by Upesh ▴ 20
ATpoint, you are absolutely bang on. In fact, my intention is not to switch careers but to connect with this field and build tools/systems …
Comment: Hifiasm is getting killed while trying to assemble a genome by pranavdatar01 • 0
I am trying to reproduce the assembly from the raw pacbio reads. I want to reconstruct the assembly using the pacbio reads only.
Comment: Does this adapter content from fastqc to warrant trimming prior to alignment? by ATpoint 89k
I would trim it. Two percent is not much but with WGS, say you have 400mio reads per sample or so, it's still millions of reads that theore…
Comment: Looking to learn practical bioinformatics by ATpoint 89k
> How do I connect the dots to a grand vision of drug discovery, DNA analysis, disease etc. Despite that computational-driven data analys…
Comment: Looking to learn practical bioinformatics by Upesh ▴ 20
Thank you, genomax, for the recommendations! Very helpful!
Comment: Learning Biology/Bioinformatic Basics by Upesh ▴ 20
For anyone landing on this page, the updated link is: [https://www.langmead-lab.org/teaching.html][1] [1]: https://www.langmead-lab.org/…
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