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515 results • Page 3 of 11
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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
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
12
votes
3
replies
2.8k
views
Tool: Hiplot: a simple and user-friendly visualization platform for scientific data
R microbial RNA-Seq visualization
updated 11 months ago by 43k • written 3.8 years ago by ▴ 130
0
votes
0
replies
530
views
Tool: Could you help us with testing/reviewing neuroscience-related webtool/database?
ion-channel database alignment nAChR
updated 11 months ago by 43k • written 3.7 years ago by • 0
0
votes
1
reply
1.8k
views
Tool: CellKb 2.0: A database of cell type marker gene sets
database marker-genes single-cell cell-types
updated 11 months ago by 43k • written 3.7 years ago by ▴ 20
72
votes
71
replies
31k
views
17 follow
Tool: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
volcano-plot bioconductor ggplot2 ggrepel
updated 11 months ago by 43k • written 5.7 years ago by 88k
6
votes
4
replies
1.0k
views
Tool: ObjTables: tools for creating and reusing high-quality spreadsheets (e.g., supplementary tables to articles)
schema-validation CSV spreadsheet XLSX
updated 11 months ago by 43k • written 3.8 years ago by ▴ 100
4
votes
4
replies
2.4k
views
Tool: kraken2table, an analogous to kaiju2table
kaiju classification kraken taxonomy
updated 11 months ago by 43k • written 3.8 years ago by ★ 3.6k
0
votes
2
replies
1.2k
views
Tool: Bioconductor PoTRA: Pathways of Topological Rank Analysis
pathyways bioconductor potra disease
updated 11 months ago by 43k • written 3.9 years ago by ▴ 50
0
votes
0
replies
950
views
Tool: Pseudotime Abstract KNetL map (PAK map) for single cell data
scrna Pseudotime graph single-cell
updated 11 months ago by 43k • written 3.8 years ago by ▴ 70
0
votes
0
replies
826
views
Tool: Summarizing clustered categorical/continuous `omics data
mutations R visualization cluster
updated 11 months ago by 43k • written 3.8 years ago by ▴ 10
3
votes
0
replies
2.8k
views
Tool: KNetL versus tSNE and UMAP for dimensionality reduction in single cell RNA-seq
UMAP dimensionality-reduction tSNE KNetL
updated 11 months ago by 43k • written 3.9 years ago by ▴ 70
2
votes
0
replies
1.6k
views
Tool: Fast and painless exploration of single-cell/bulk T-cell and antibody repertoires in R
repseq antibody immunology airr tcr
updated 11 months ago by 43k • written 3.9 years ago by ▴ 90
0
votes
1
reply
1.2k
views
Tool: SPACE: a web tool for exploring chromatin accessibility in cancers based on ATAC-seq
database chromatin-accessibility ATAC-seq
updated 11 months ago by 43k • written 4.0 years ago by • 0
2
votes
0
replies
1.4k
views
Tool: CIPR - Cluster Identity Predictor for scRNAseq experiments
scRNAseq R RNA-Seq shiny
updated 11 months ago by 43k • written 4.0 years ago by ▴ 310
2
votes
0
replies
912
views
Tool: Corona OMA Browser: orthologs among corona viruses including SARS-COV-1 and SARS-COV-2
orthologs comparative-genomics phylogenetics
updated 11 months ago by 43k • written 3.9 years ago by ▴ 740
4
votes
7
replies
1.4k
views
Tool: Elloreas, a new genome assembler
Assembly next-gen
updated 11 months ago by 43k • written 3.9 years ago by ★ 1.2k
3
votes
1
reply
7.5k
views
Tool: Weeder 2.0 - motif discovery tool updated
motif-discovery chip-seq weeder
updated 11 months ago by 43k • written 9.6 years ago by 6.0k
3
votes
1
reply
984
views
Tool: Simplify Your Sample Annotation and Submission Using METAGENOTE
COVID-19 genome metadata sequencing
updated 11 months ago by 43k • written 4.7 years ago by ▴ 60
6
votes
0
replies
2.0k
views
Tool: BioTuring Big Data: a new portal for reanalyzing large public single-cell RNA-seq data sets
scRNA-seq RNA-Seq single-cell
updated 11 months ago by 43k • written 4.1 years ago by ▴ 450
2
votes
0
replies
683
views
Tool: ToolDirectory: dynamic visualization of softwares managed by a Bioinformatics Core Facility
edam visualisation
updated 10 months ago by 43k • written 4.0 years ago by ▴ 140
5
votes
0
replies
1.1k
views
Tool: TidyWrappers : an R package to deal with an object tbl
ChIP-Seq wrappers R RNA-Seq gene-expression
updated 11 months ago by 43k • written 4.1 years ago by ★ 2.0k
3
votes
0
replies
1.1k
views
Tool: Sars-Cov-2 Genome & ACE 2 Exploration
sequence alignment SNP genome
13 days ago by Ibrahim Tanyalcin ★ 1.2k
0
votes
0
replies
1.0k
views
Tool: use IGV to visualize sc-ChIP-seq
signal-cell ChIP-Seq
updated 11 months ago by 43k • written 4.1 years ago by • 0
11
votes
5
replies
2.6k
views
Tool: A resource with diverse databases and tools for SARS-CoV-2 (COVID-19) bioinformatics -- Updates
SARS-CoV-2 Corona Databases COVID-19
updated 11 months ago by 43k • written 4.2 years ago by ▴ 270
0
votes
0
replies
875
views
Tool: GSOAP: a tool for visualization of gene set over-representation analysis
R enrichment-analysis visualisation
updated 11 months ago by 43k • written 4.2 years ago by ▴ 50
0
votes
0
replies
723
views
Tool: UniprotR package Feedback
R
updated 11 months ago by 43k • written 4.2 years ago by • 0
4
votes
3
replies
2.0k
views
Tool: shinyChromosome: an R/Shiny application for interactive creation of non-circular plots of whole genome
R genome shiny
updated 11 months ago by 43k • written 5.8 years ago by ▴ 110
2
votes
5
replies
3.2k
views
Tool: Gencove Open and free API. Any DNA data from any type to VCF in 10 to 30 mins.
VCF API imputation
updated 11 months ago by 43k • written 6.6 years ago by ▴ 30
7
votes
3
replies
2.5k
views
Tool: methplotlib: visualization and analysis of modified nucleotides from nanopore sequencing
nanopore methylation sequencing
updated 11 months ago by 43k • written 4.2 years ago by 47k
6
votes
4
replies
1.4k
views
Tool: ctDNAtools: an R package to work with ctDNA sequencing data
cancer-genomics ngs liquid-biopsy sequencing ctdna
updated 11 months ago by 43k • written 4.3 years ago by ▴ 100
1
vote
4
replies
2.8k
views
Tool: Circle-Map: Sensitive detection of circular DNA at single-nucleotide resolution using guided realignment of partially aligned reads
circDNA ecDNA eccDNA
updated 11 months ago by 43k • written 5.0 years ago by ▴ 760
6
votes
0
replies
1.6k
views
Tool: Hera-T: an efficient and accurate algorithm for quantifying single-cell UMI count data
scRNA-seq single-cell RNA-Seq
updated 11 months ago by 43k • written 5.1 years ago by ▴ 450
13
votes
8
replies
4.3k
views
Tool: MSigDB for Multiple Organisms in a Tidy Data Format
msigdb pathways R gsea
updated 11 months ago by 43k • written 6.1 years ago by 13k
1
vote
0
replies
805
views
Tool: MutaFrame - ORF finder
sequence protein gene
updated 11 months ago by 43k • written 4.4 years ago by ★ 1.2k
3
votes
0
replies
1.3k
views
Tool: Omics Playground: a comprehensive self-service platform for visualization, analytics and exploration of Omics Data
expression-data scRNA-seq RNA-Seq NGS
updated 11 months ago by 43k • written 4.4 years ago by ▴ 30
515 results • Page 3 of 11
Recent Votes
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?
Answer: ChatGPT optimized for bioinformatics questions
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Popular Question to synat.keam ▴ 100
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Recent Replies
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.
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…
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