Limit : all time
all time today this week this month this year
735 results • Page 3 of 15
Sort: Rank
Rank Views Votes Replies
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
2.0 years ago by Michael 54k
2
votes
0
replies
594
views
Tool: Introducing ElasticBLAST – Run bigger BLAST searches faster on the Cloud
ElasticBLAST BLAST NCBI
updated 11 months ago by 43k • written 2.1 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
7.0k
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 6.2 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
2.3 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
920
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
2.7k
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
730
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
683
views
Tool: Genotype Imputation Workflow
gwas imputation.
2.6 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
986
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 10.6 years ago by ▴ 450
1
vote
0
replies
581
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
553
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
997
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 3.5 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
0
votes
0
replies
545
views
Tool: Unicorn Papers - Top ‱ cited papers from PUBMED
citation paper research PUBMED bibliometrics
2.9 years ago by Lukasz Kozlowski • 0
4
votes
7
replies
4.6k
views
6 follow
Tool: MAGERI: a software tool for calling rare variants and detecting circulating tumor DNA from UMI-tagged high-throughput sequencing data
rare-variant resequencing umi ctDNA
updated 3 months ago by • 0 • written 7.0 years ago by 3.5k
735 results • Page 3 of 15
Recent Votes
Answer: featureCounts output summary assigned value higher than uniquely mapped reads fr
Answer: Doubt about the process of annotation, detection, identification and classificat
Answer: Filtering VCF files based on VAF giving incorrect results
Problems with breakdancer (sv caller) output.
Problems with breakdancer (sv caller) output.
Comment: Add stats to boxplot in R
Answer: Genotyping sites with N in reference genome
Recent Locations • All
Iran, just now
United States, just now
United States, just now
USA/New York/The Rockefeller University, 2 minutes ago
United Kingdom, 4 minutes ago
Syracuse, NY, United States, 5 minutes ago
Morocco, 5 minutes ago
Recent Awards • All
Scholar to Prawesh • 0
Popular Question to Jean-Karim Heriche 27k
Popular Question to Chironex ▴ 40
Scholar to rpolicastro 13k
Popular Question to Amr ▴ 160
Popular Question to asalimih ▴ 60
Popular Question to nd48 ▴ 20
Recent Replies
Comment: Filtering VCF files based on VAF giving incorrect results by Pierre Lindenbaum 161k
> Do you think my commands were correct? I'm not familiar enough with this bcftools syntax. but what if there is no AD, what if both…
Answer: How can you *consistently* download BioProject IDs from NCBI's BioSample databas by Ash • 0
I know this was asked several years ago, but finding this post helped me solve my own problem and in the process I solved this one too. …
Answer: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by swbarnes2 14k
Would Parkinson's be expected to have an effect on blood cells? Neurons, sure, but blood cells?
Comment: Doubt about the process of annotation, detection, identification and classificat by MarcosCosta • 0
Thank you very much, you've helped me a lot. Could you suggest a book or article that offers a complete explanation of these processes?
Comment: Filtering VCF files based on VAF giving incorrect results by Arton • 0
Thank you. I can't try a completely new tool but I will keep your command for future use. Do you think my commands were correct? For exampl…
Comment: Add stats to boxplot in R by Ghada • 0
Thanks. Thats work
Comment: Genotyping sites with N in reference genome by Zhenyu Zhang ★ 1.2k
Whether N -> A/T/G/C represents a variant is heavily dependent on the tool itself, and I know most tools don't. Since you don't see it in y…
Comment: calculating genomic coverage/ base overlap in R by marco.barr ▴ 110
The code seems correct at first glance... How did you generate the data in the Excel file? Have you checked the exon annotations? You could…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by GenoMax 142k
Did you remeber to unzip/untar the `nt` preformatted files that you downloaded?
Comment: Genotyping sites with N in reference genome by shpak.max ▴ 50
Just to clarify, I have set additional sites in the reference genome to 'N', which means (based on your statement) that these will not be g…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by Pierre Lindenbaum 161k
see https://www.biostars.org/p/9496674/ <!-- when i runed blastn(version 2.15) and nt database(latest version). I used aspera to download…
Answer: Genotyping sites with N in reference genome by Pierre Lindenbaum 161k
> Does UnifiedGenotyper skip/ignore sites where the reference genotype is N yes. The variant is in YOUR data, not in the reference where '…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline? by yura.grabovska ▴ 70
Do you have samples that should in theory have a good degree over overlap in terms of cell types across the two sequencing types? I would …
Comment: Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file by asalimih ▴ 60
I found out that vep is only checking the GT field therefore assigning HOM to the Zygosity. Therefore the problem should be from deepvarian…
Comment: Add stats to boxplot in R by Lélé ▴ 10
To remove "Kruskall Wallis" you can try adding the argument label="p" or label = "p.signif" which displays the p-value or *** like this: …
Traffic: 2924 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6