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736 results • Page 4 of 15
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545
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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
1
vote
0
replies
600
views
Tool: Super easy to use free paper retrieval artifact: PyPubMed
python pubmed software
updated 11 months ago by 43k • written 3.0 years ago by ▴ 420
0
votes
0
replies
681
views
Tool: Help solve the cancer puzzle & benefit your research! SimBioSys PhenoScope for integrative multi-modal and multi-omic data analytics
multi-modal multi-omic breast analytics cancer imaging
3.0 years ago by johnpfeiffer • 0
0
votes
0
replies
609
views
Tool: SimBioSys PhenoScope - a cloud-based multi-modal multi-omic data analytics platform for oncology researchers
cloud-based analytic cancer multi-modal multi-omic
3.0 years ago by johnpfeiffer • 0
0
votes
0
replies
702
views
Tool: IPC 2.0: prediction of isoelectric point and pKa dissociation constants
deep-learning isoelectric-point 2D-PAGE pKa
updated 11 months ago by 43k • written 3.0 years ago by • 0
8
votes
6
replies
5.9k
views
Tool: chromoMap- R package for Interactive visualization and Annotation of chromosomes or regions of any living organism.
annotation R genome visualization
updated 11 months ago by 43k • written 5.1 years ago by ▴ 80
0
votes
0
replies
558
views
Tool: Omics Playground Cloud Version
RNA-seq Transcriptomics scRNA-seq Proteomics
3.0 years ago by Axel Martinelli • 0
2
votes
1
reply
887
views
Tool: Complex heatmaps
R heatmap customize
updated 3.0 years ago by 82k • written 3.0 years ago by ★ 27k
13
votes
14
replies
6.2k
views
9 follow
Tool: open-cravat: variant annotation tool
open-cravat
updated 11 months ago by 43k • written 5.4 years ago by ▴ 260
6
votes
3
replies
4.9k
views
Tool: Clustering of short peptide sequences
peptide phage-display clustering
updated 20 months ago by 43k • written 8.6 years ago by ▴ 420
2
votes
1
reply
779
views
Tool: Bioinformatics Programming Package
Package
updated 11 months ago by 43k • written 3.1 years ago by ▴ 10
68
votes
25
replies
16k
views
12 follow
Tool: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
fastq SRA
updated 6 months ago by 142k • written 5.2 years ago by ★ 1.4k
3
votes
1
reply
2.8k
views
Tool: VCF2PopTree: build a phylogenetic tree from a VCF file
VCF2Phylogenetictree
updated 3.1 years ago by ▴ 490 • written 3.2 years ago by ▴ 60
2
votes
0
replies
671
views
Tool: New Tuberculosis in 3D Interactive Viewer
tuberculosis viewer 3D
3.2 years ago by karlynn.noble ▴ 60
2
votes
0
replies
863
views
Tool: New location tracking tool for SARS-CoV-2 variant surveillance
sars-cov-2 variant covid-19
updated 11 months ago by 43k • written 3.2 years ago by ▴ 20
12
votes
5
replies
6.2k
views
Tool: AGAT - Another Gff/Gtf Analysis Toolkit
gff gtf
updated 10 months ago by 43k • written 4.4 years ago by 8.6k
18
votes
39
replies
4.3k
views
Tool: CBioInfCpp.h as a C++ lib containing some functions for bioinformatics
cpp
updated 12 months ago by 43k • written 5.1 years ago by ▴ 50
3
votes
1
reply
1.3k
views
Tool: Introducing Gallia: a Scala library for data manipulation
scala etl json vcf spark
updated 11 months ago by 43k • written 3.3 years ago by ▴ 30
0
votes
0
replies
1.4k
views
Tool: I made QMplot: a python library and tools of generating high-quality manhattan and Q-Q plots for GWAS data
visualization Manhattan-Plot GWAS genome Python
updated 11 months ago by 43k • written 3.2 years ago by • 0
15
votes
2
replies
3.1k
views
Tool: EnhancedVolcano becomes a pseudo-EnhancedMA
enhancedMA enhancedvolcano
updated 11 months ago by 43k • written 3.7 years ago by 88k
4
votes
1
reply
1.3k
views
Tool: rBCS & pyBCS: open-source packages to support interactive visualizations of single-cell data
rna-seq single-cell scrna-seq
updated 11 months ago by 43k • written 3.2 years ago by ▴ 450
0
votes
0
replies
673
views
Tool: MultiLink Analysis: Brain Network Comparison via Sparse Connectivity Analysis
networks neuroscience connectome brain
updated 11 months ago by 43k • written 3.3 years ago by • 0
1
vote
0
replies
681
views
Tool: BiOkeanos - the largest(*) biomedical database catalogue and discovery tool
database catalogue data
updated 11 months ago by 43k • written 3.3 years ago by ▴ 20
0
votes
0
replies
844
views
Tool: Analyze & Visualize Nephele Microbiome Results Using MicrobiomeDB
microbiome sequence
updated 11 months ago by 43k • written 3.3 years ago by ▴ 60
22
votes
20
replies
4.9k
views
Tool: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
sam bam bqsr
updated 11 months ago by 43k • written 5.6 years ago by ▴ 150
7
votes
10
replies
1.5k
views
Tool: SamReadViewer - A small utility to visualise read alignment directly from sam format without reference.
samreadviewer
updated 11 months ago by 43k • written 3.6 years ago by 8.6k
0
votes
0
replies
632
views
Tool: Cytoscape Network analysis
software-error cytoscape
updated 11 months ago by 43k • written 3.3 years ago by • 0
0
votes
3
replies
799
views
Tool: Script: Getting information about SRX experiment ID from NCBI database
next-gen RNA-Seq
updated 15 months ago by 43k • written 3.3 years ago by • 0
0
votes
6
replies
1.5k
views
Tool: Script: Downloading fastq files from ENA database
next-gen-sequencing RNA-Seq
updated 11 months ago by 43k • written 3.3 years ago by • 0
11
votes
2
replies
7.1k
views
Tool: fastp (the ultra-fast all-in-one FASTQ preprocessing tool) v0.18.0 released, 2X faster, with many new features.
fastp QC
updated 11 months ago by 43k • written 5.9 years ago by ★ 2.5k
4
votes
2
replies
1.1k
views
Tool: Alternate the wild type and mutant of SARS-CoV-2 N501Y
SNP
updated 11 months ago by 43k • written 3.4 years ago by ▴ 370
24
votes
26
replies
3.7k
views
Tool: ClinCNV: CNV detection from short reads
variant-calling cna cnv
updated 11 months ago by 43k • written 4.6 years ago by ★ 2.9k
79
votes
86
replies
32k
views
20 follow
Tool: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
clumpify storage bbmap pigz compression
updated 11 months ago by 43k • written 7.5 years ago by 20k
34
votes
30
replies
3.0k
views
6 follow
Tool: BioFlows - Container-enabled Bioinformatics pipeline engine
workflow next-gen RNA-Seq pipeline
updated 14 months ago by 43k • written 3.4 years ago by ▴ 90
2
votes
3
replies
1.4k
views
Tool: Filtering BAM files efficiently
BAM genome SAM alignment
updated 11 months ago by 43k • written 3.5 years ago by • 0
2
votes
1
reply
1.2k
views
Tool: Alternate wild type and mutant of SNPs in 3D
Jupyter-Notebook iCn3D SNP 3D-viewer
updated 11 months ago by 43k • written 3.8 years ago by ▴ 370
3
votes
0
replies
888
views
Tool: ChromSCape - A R/Shiny application to analyze single-cell epigenomics data
ChIP-Seq R scChIP-seq scATAC-seq single-cell
updated 11 months ago by 43k • written 3.5 years ago by ▴ 120
2
votes
0
replies
770
views
Tool: driveR - Prioritizing Cancer Driver Genes Using Genomics Data
R driver-gene cancer
updated 11 months ago by 43k • written 3.5 years ago by ★ 1.3k
1
vote
2
replies
1.1k
views
Tool: Graphia: A platform for the graph-based visualisation and analysis of complex data
networks high-dimensional-data transcriptomics
updated 11 months ago by 43k • written 3.6 years ago by ▴ 10
3
votes
0
replies
982
views
Tool: Trimviz, a lightweight QC tool to assess impact of read-trimming and aligner soft-clipping
alignment trimming QC clipping fastq
updated 11 months ago by 43k • written 3.6 years ago by ▴ 140
1
vote
0
replies
961
views
Tool: Introducing WARP: A collection of cloud-optimized workflows for biological data processing and analysis
wdl workflows genomics epigenomics single-cell
updated 11 months ago by 43k • written 3.6 years ago by ★ 1.2k
31
votes
22
replies
13k
views
6 follow
Tool: SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
FASTQ SeqKit FASTA
updated 11 months ago by 43k • written 7.6 years ago by 8.5k
2
votes
1
reply
1.1k
views
Tool: Machine learning Python API for ligand-protein binding-affinity prediction
machine-learning binding-affinity R api python
updated 11 months ago by 43k • written 3.6 years ago by ▴ 20
1
vote
1
reply
949
views
Tool: PathogenAR - Structural Biology in Augmented Reality
augmented-reality influenza pathogen
updated 11 months ago by 43k • written 3.9 years ago by ▴ 60
56
votes
52
replies
50k
views
12 follow
Tool: Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF Gene-Clustering
updated 11 months ago by 43k • written 9.8 years ago by 7.5k
0
votes
3
replies
1.5k
views
Tool: New data transformation tool for Windows and Mac
data-wrangling software data-munging
updated 11 months ago by 43k • written 3.8 years ago by • 0
4
votes
1
reply
3.9k
views
Tool: kg: query kegg from the command line
kegg kg
updated 11 months ago by 43k • written 8.9 years ago by ▴ 960
4
votes
0
replies
918
views
Tool: Fix Prokka fragmented gene annotations - Long read assembly
fragmented-gene-annotation Prokka
updated 11 months ago by 43k • written 3.6 years ago by 8.6k
0
votes
0
replies
860
views
Tool: SimpleITK Version 2.0 Now Available
segmentation registration imaging
updated 11 months ago by 43k • written 3.6 years ago by ▴ 60
736 results • Page 4 of 15
Recent Votes
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
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Popular Question to Muhammad • 0
Popular Question to synat.keam ▴ 100
Scholar to jv ★ 1.8k
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Recent Replies
Answer: Checking chromosome builds for genotyping data by Muhammad • 0
Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors) by nguyenn6 • 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed by anton.i.petrov • 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp by analyst ▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by GenoMax 142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R by 1769mkc ★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks by ATpoint 82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner by Joe 21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression? by Gordon Smyth ★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF) by aidangcruickshank ▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
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.
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