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736 results • Page 3 of 15
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76
votes
14
replies
13k
views
10 follow
Tool: karyoploteR: uncircle your genomes
karyoploteR Rdataviz NGS
updated 11 months ago by 43k • written 6.9 years ago by ★ 3.4k
0
votes
0
replies
423
views
Tool: Announcing the Papilloma Virus Episteme (PaVE) 2.0 Release
genomics HPV 3D
2.1 years ago by karlynn.noble ▴ 60
0
votes
0
replies
399
views
Tool: Nature Communications: New AI tool for in-depth cleaning of a wide range of noise in single-cell RNA-Seq data
denoise scRNA-Seq AutoClass AI
2.1 years ago by bigmawen ▴ 430
9
votes
7
replies
1.7k
views
Tool: miniDBG - a Jupyter notebook for teaching De Bruijn Graph assembly
python deBruijnGraph de_bruijn_graph assembly teaching
2.1 years ago by Michael 54k
2
votes
0
replies
595
views
Tool: Introducing ElasticBLAST – Run bigger BLAST searches faster on the Cloud
ElasticBLAST BLAST NCBI
updated 11 months ago by 43k • written 2.2 years ago by ▴ 410
1
vote
1
reply
609
views
Tool: New VCF Header (schema) Parser---Please Break!!!
VCF header
updated 2.2 years ago by ★ 2.9k • written 2.2 years ago by ▴ 250
231
votes
38
replies
146k
views
29 follow
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl genome-coordinates liftover
updated 11 months ago by 43k • written 11.2 years ago by 20k
5
votes
2
replies
2.4k
views
Tool: eLabFTW: a free and open source electronic lab notebook
elabftw free-open-source-software php
updated 11 months ago by 43k • written 4.7 years ago by ▴ 190
1
vote
1
reply
3.7k
views
Tool: mirDIP 4.1 - integrative database of human microRNA target predictions
interactome miRNA targets microRNA
updated 11 months ago by 43k • written 6.0 years ago by ▴ 50
2
votes
6
replies
3.4k
views
Tool: microbiomeMarker: microbiome biomarker analysis in R
stamp microbiome lefse
updated 11 months ago by 43k • written 3.9 years ago by ▴ 30
5
votes
8
replies
7.1k
views
6 follow
Tool: Converting MUMmer snps file to a real VCF file
VCF mummer SNP
updated 11 months ago by 43k • written 4.7 years ago by ★ 3.6k
4
votes
3
replies
1.2k
views
Tool: Make a Sequence Logo in your browser by using native Javascript.
javascript sequence browser logo
2.3 years ago by Paul A. Gagniuc ▴ 30
0
votes
0
replies
469
views
Tool: Local sequence alignment made visual in your browser
javascript browser sequence alignment local
2.2 years ago by Paul A. Gagniuc ▴ 30
15
votes
11
replies
8.3k
views
Tool: Arriba: Fast and accurate gene fusion detection from RNA-Seq data
variant-calling RNA-Seq cancer gene-fusion
updated 11 months ago by 43k • written 6.3 years ago by ▴ 150
0
votes
0
replies
482
views
Tool: AIQC - open source framework making deep learning accessible for researchers.
statistics machine multi-omic learning ai
2.4 years ago by Kermit ▴ 90
28
votes
17
replies
5.1k
views
7 follow
Tool: PCAtools: everything Principal Components Analysis
eigenvector pca bioconductor R
updated 11 months ago by 43k • written 5.3 years ago by 88k
13
votes
7
replies
4.2k
views
Tool: I-PV: a CIRCOS module for interactive protein sequence visualization
interactive javascript circos sequence
updated 21 months ago by 43k • written 8.6 years ago by ★ 1.2k
0
votes
1
reply
685
views
Tool: Molecular Dynamics analysis tools [desmond Schrodinger]
dynamics schrodinger desmond mdanalysis molecular
updated 2.5 years ago by 142k • written 2.5 years ago by • 0
0
votes
0
replies
518
views
Tool: SBGNview published online with Bioinformatics
Pathview BioConductor SBNGview visualization pathway
2.5 years ago by bigmawen ▴ 430
10
votes
5
replies
2.5k
views
Tool: Genozip: A new compression tool for FASTQ, BAM, VCF and more
bam vcf fastq compression
10 months ago by Divon ▴ 230
0
votes
0
replies
443
views
Tool: Proteome-pI 2.0 - Proteome Isoelectric Point Database
isoelectric_point protein pKa database proteomics
2.5 years ago by Lukasz Kozlowski • 0
4
votes
13
replies
2.8k
views
Tool: SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
pathway-analysis visualization Pathview SBGN
updated 11 months ago by 43k • written 3.2 years ago by ▴ 430
1
vote
1
reply
923
views
Tool: Cell Type Prediction - covering 45 immune cell types
citeseq scRNA singlecell
updated 2.6 years ago by ▴ 50 • written 2.7 years ago by ▴ 580
3
votes
5
replies
2.8k
views
Tool: Extend 3' UTR of a GTF file
annotation python RNA-Seq GTF
updated 11 months ago by 43k • written 3.6 years ago by ★ 1.4k
10
votes
1
reply
1.5k
views
Tool: fastp 0.23.0 released, runs 2x faster, and generates reproducible outputs.
FASTQ
updated 2.6 years ago by 142k • written 2.6 years ago by ★ 2.5k
1
vote
0
replies
599
views
Tool: A pairwise genome alignment pipeline using LAST and Nextflow
genome LAST Nextflow dotplot alignment
2.6 years ago by Charles Plessy ★ 2.9k
0
votes
0
replies
590
views
Tool: NGS-Barcode-Count
DEL NGS CRISPRseq
2.6 years ago by coffeyrt • 0
0
votes
0
replies
1.3k
views
Tool: Utilising QIIME 2 pipeline: a current and future golden standard platform to analyze Amplicon-Seq data
NGS Sequencing
updated 15 months ago by 43k • written 2.6 years ago by ▴ 420
4
votes
0
replies
731
views
Tool: Annoyed by contig name inconsistencies (eg chr22 vs 22)? A solution
contigs bam vcf reference compression
2.6 years ago by Divon ▴ 230
0
votes
0
replies
684
views
Tool: Genotype Imputation Workflow
gwas imputation.
2.7 years ago by nhaus ▴ 360
1
vote
0
replies
497
views
Tool: shell script to search txt in academic figures
search_txt_in_image.sh
2.7 years ago by Zhilong Jia ★ 2.2k
0
votes
0
replies
1.1k
views
Tool: Still Not Use QIIME2 for Amplicon Analysis? You’re OUT!
NGS Sequencing
updated 15 months ago by 43k • written 2.7 years ago by ▴ 420
1
vote
2
replies
988
views
Tool: krust: a k-mer counter in Rust using the rust-bio and rayon crates
Rust kmer-counting fasta kmer
updated 2.7 years ago by 100k • written 2.7 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Tool: BioFileConverter - an app for Mac users to convert .xdna and .dna files into genbank .gb files and more
dna genbank xdna
updated 14 months ago by 43k • written 2.7 years ago by ▴ 180
4
votes
3
replies
1.4k
views
Tool: brename: safely batch renaming files/directories via regular expression
batch renaming
updated 2.7 years ago by 43k • written 2.7 years ago by 8.5k
0
votes
0
replies
1.2k
views
Tool: Handy online tool for genomic analysis and data visualization - Part II
NGS Sequencing
updated 14 months ago by 43k • written 2.7 years ago by ▴ 420
1
vote
0
replies
519
views
Tool: Looking for feedback on epigenetics R package - enhancer detection and visualization
epigenetics chromatin enhancers atac chip
2.7 years ago by Alex ▴ 20
0
votes
0
replies
563
views
Tool: A framework to prioritize miRNA-driven post-transcriptional signals using exonic and intronic regions of RNAseq data
post-transcriptional miRNA intron exon RNAseq
2.7 years ago by Emilio Marmol ▴ 170
50
votes
16
replies
14k
views
12 follow
Tool: Omictools: A didactic directory for omic data analysis (NGS, microarray, PCR, MS, NMR)
pcr software ngs
updated 11 months ago by 43k • written 10.7 years ago by ▴ 450
1
vote
0
replies
583
views
Tool: Omics Playground: visualization and analysis of transcriptomics and proteomics data
proteomics RNA RNA-seq scRNA-seq omics data
2.8 years ago by bigomics.team ▴ 90
2
votes
2
replies
1.0k
views
Tool: miRAnno—network-based functional microRNA annotation
pathways miRNA annotation microRNA
2.8 years ago by tomastokar ▴ 50
21
votes
14
replies
9.5k
views
Tool: trackplot: Fast and minimal dependency standalone R script to generate IGV style locus tracks from bigWig files
visualization igv ChIP-Seq R bigwigs
updated 11 months ago by 43k • written 3.5 years ago by ★ 3.2k
1
vote
0
replies
2.0k
views
Tool: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
biomart annotation Ensembl
2.8 years ago by Shred ★ 1.4k
1
vote
0
replies
554
views
Tool: BIRCH Bioinformatics System v3.80
alignment RNA-seq genome assembly sequence phylogeny
2.8 years ago by brian.fristensky ▴ 460
0
votes
0
replies
589
views
Tool: Manticore: a software to extract the intermixed regions of subgenomes in hybrid species
mapping hybrid subgenome genomics sequencing
2.8 years ago by Matteo Schiavinato ★ 3.6k
3
votes
1
reply
1.2k
views
Tool: all2vcf: a tool to convert non-standard variant outputs (mummer. bcftools isec) to VCF
mummer isec variant bcftools VCF
updated 18 months ago by • 0 • written 2.8 years ago by ★ 3.6k
0
votes
0
replies
999
views
Tool: Handy online tool for genomic analysis and data visualization - Part I
NGS Sequencing
updated 14 months ago by 43k • written 2.8 years ago by ▴ 420
2
votes
0
replies
668
views
Tool: metaGEM: create your own genome scale metabolic models directly from metagenomes
metagenomics metagenome-assembled-genome genome-scale-metabolic-model metabolism
updated 2.8 years ago by 43k • written 2.8 years ago by ▴ 20
9
votes
7
replies
3.0k
views
Tool: DiffBind 3.0: Extensive updates in Bioconductor 3.12
DiffBind ChIP-Seq diffbind ATAC-seq chipseq
updated 11 months ago by 43k • written 3.6 years ago by ★ 2.0k
0
votes
1
reply
1.1k
views
Tool: Compi: Application Framework for Portable Computational Pipelines
pipeline workflow-management-system docker
updated 11 months ago by 43k • written 4.6 years ago by ▴ 380
736 results • Page 3 of 15
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A: Peaks And Nearby Genes
Answer: How to download dbSNP153 vcf files in hg19/GRCH37 version
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Answer: TFs and Gene databases
A: Is there a software that can compare phylogenetic trees to each othe (face to fa
Comment: Differentially Expressed Genes between two conditions (scRNA, single GEO dataset
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Recent Replies
Comment: How to handle duplicated genes in TCGA data? by Ngrin • 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot by LauferVA 4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot by bk11 ★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool by ntsopoul ▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool by GenoMax 142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by bk11 ★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs by dthorbur ★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: how to treat the replicates while performing WGCNA by andres.firrincieli 3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated by alanh ▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data? by Zhenyu Zhang ★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by Ram 43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs by BATMAN • 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
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