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Tool: Introducing WARP: A collection of cloud-optimized workflows for biological data processing and analysis

epigenomics tool genomics single-cell workflows wdl written 1 day ago by vdauwera • 970

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5.4k

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Tool: SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

fasta fastq seqkit tool written 4.1 years ago by shenwei356 ♦ 5.5k • updated 10 days ago by adriana.gallego.02 • 10

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104

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Tool: Machine learning Python API for ligand-protein binding-affinity prediction

tool python machine learning R binding-affinity api written 13 days ago by casey • 20

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173

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Tool: PathogenAR - Structural Biology in Augmented Reality

influenza augmented reality pathogen tool written 4 months ago by karlynn.noble • 40

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33k

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61 follow

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Tool: Gene Set Clustering based on Functional annotation (GeneSCF)

genescf gene clustering based on function tool written 6.2 years ago by EagleEye ♦ 6.7k

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273

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Tool: New data transformation tool for Windows and Mac

software data munging data wrangling tool written 3 months ago by andy • 0 • updated 21 days ago by cheapseo • 0

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2.3k

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Tool: kg: query kegg from the command line

kg kegg tool written 5.3 years ago by Endre Bakken Stovner • 890 • updated 22 days ago by RamRS ♦ 30k

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138

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Tool: SamReadViewer - A small utility to visualise read alignment directly from sam format without reference.

viewer read sam tool written 22 days ago by Juke34 • 4.8k

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149

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Tool: Extend 3' UTR of a GTF file

gtf annotation tool rna-seq python written 25 days ago by Shred • 220

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110

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Tool: Fix Prokka fragmented gene annotations - Long read assembly

gene annotation tool prokka fragmented written 28 days ago by Juke34 • 4.8k

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4.0k

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27 follow

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Tool: sra-explorer : find SRA and FastQ download URLs in a couple of clicks

sra fastq tool sequence-read-archive download written 20 months ago by Phil Ewels • 600 • updated 27 days ago by ATpoint ♦ 40k

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107

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Tool: SimpleITK Version 2.0 Now Available

imaging analysis segmentation registration tool written 4 weeks ago by karlynn.noble • 40

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865

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Tool: Hiplot: a simple and user-friendly visualization platform for scientific data

R visualization microbial rna-seq tool written 10 weeks ago by Hiplot • 110

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3.4k

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21 follow

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Tool: pathfindR - Enrichment Analysis using Active Subnetworks

pathway R active subnetwork tool enrichment written 2.6 years ago by egeulgen • 1000

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616

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Tool: SEDA (SEquence DAtaset builder): a desktop tool for processing FASTA files containing DNA and protein sequences

fasta bioinformatics java sequences tool written 10 months ago by Hugo • 290

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135

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Tool: Could you help us with testing/reviewing neuroscience-related webtool/database?

tool software error database alignment nachr ionchannel written 7 weeks ago by chareshneu.tech • 0

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181

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Tool: CellKb 2.0: A database of cell type marker gene sets

single-cell database marker genes tool cell types written 7 weeks ago by Ashwini Patil • 10

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530

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11 follow

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Tool: EnhancedVolcano becomes a pseudo-EnhancedMA

enhancedvolcano enhancedma tool written 8 weeks ago by Kevin Blighe ♦ 66k

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9.8k

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51 follow

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Tool: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling

bioconductor ggplot2 ggrepel tool volcano plot written 2.1 years ago by Kevin Blighe ♦ 66k

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1.5k

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14 follow

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Tool: PCAtools: everything Principal Components Analysis

R bioconductor pca eigenvector tool written 20 months ago by Kevin Blighe ♦ 66k

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2.3k

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Tool: New Mac program for molecular biologists

software tool written 15 months ago by vytarasov • 110

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222

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Tool: ObjTables: tools for creating and reusing high-quality spreadsheets (e.g., supplementary tables to articles)

xlsx tool schema csv spreadsheet validation written 11 weeks ago by jonrkarr • 100

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211

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Tool: kraken2table, an analogous to kaiju2table

kraken kaiju taxonomy classification tool written 11 weeks ago by Macspider • 3.2k

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229

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Tool: Bioconductor PoTRA: Pathways of Topological Rank Analysis

bioconductor pathyways disease potra tool written 4 months ago by plink_9857 • 50

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114

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Tool: (Closed) ligand based drug designing

tool drug designing selex drug design aptamer aptamers written 12 weeks ago by jnvabhigna123 • 0

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184

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Tool: View SNPs of SARS-Cov-2 structures in iCn3D viewer and Jupyter Notebook

jupyter notebook 3d viewer icn3d snp tool written 3 months ago by Jiyao Wang • 0

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148

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Tool: Pseudotime Abstract KNetL map (PAK map) for single cell data

pseudotime scrna tool graph single cell written 3 months ago by alireza.khodadadi.j • 60

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194

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Tool: Summarizing clustered categorical/continuous `omics data

cluster R visualization tool mutations written 3 months ago by arshiaurora • 10

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291

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Tool: KNetL versus tSNE and UMAP for dimensionality reduction in single cell RNA-seq

tsne knetl dimensionality reduction umap tool written 4 months ago by alireza.khodadadi.j • 60

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1.3k

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Tool: CBioInfCpp.h as a C++ lib containing some functions for bioinformatics

c++ tool written 18 months ago by chernouhov sergey • 50

Recent Votes

Recent Locations • All »

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Scholar to ATpoint ♦ 40k
Appreciated to Istvan Albert ♦♦ 85k
Scholar to jmath97 • 0
Teacher to Mensur Dlakic • 6.9k
Teacher to a.alnawfal.1992 • 80
Teacher to ATpoint ♦ 40k

Recent Replies

C: Limma for metabolomics data by newbio17 • 240
I'm late to the party, but I wanted to add a comment on scaling the data prior to limma analysis ...
C: Convert amino acids to nucleotides in linux by Fatima • 740
These links may help: https://www.biostars.org/p/421074/ https://www.ebi.ac.uk/Tools/st/emboss...
C: Way to check if gene A lies in the same ORF as gene B by Fatima • 740
Hi! Could you provide an example?
C: How to change font size and color in HallmarkPathway Analysis with fgsea ? by ATpoint ♦ 40k
It is a ggplot-based plot, so please google for help towards ggplot parameters. This is basic R, ...
C: HISAT2: Question regarding providing file path to indexed genome folder by venura • 60
Everything is running fine and got bam files too. :) The only exception is the following (I guess...
A: How to create bigwig using mm10.fasta and mm10.fasta bowtie index files by elbakri.fatimazahrae • 0
the error is src/util/mappability/internal/fastaToRead missing, try recompiling..., getting...
A: How to create bigwig using mm10.fasta and mm10.fasta bowtie index files by elbakri.fatimazahrae • 0
I get the same error, I reinstalled and recompiling but still have the same error how should I fi...
C: Is it possible to retrieve the original reads from a BAM file? by ATpoint ♦ 40k
There are multiple suggestions on how to do this in this thread. Suggest you pick one and try it.
A: Blastdbcmd (Windows) - Too Many Positional Arguments by h.mon ♦ 31k
As https://www.biostars.org/u/1969/ , I suspect the variable `$db` is empty, so blastp interprets...
C: Is it possible to retrieve the original reads from a BAM file? by bazghazia7 • 0
where you able to retrieve your original reads file frombam files? Can you share the processs and...
C: HISAT2: Question regarding providing file path to indexed genome folder by venura • 60
Oh, Shoot! You are correct. Still learning A, B, Cs..
C: Individual genes plots after batch correction with Deseq2 by fanimata • 0
Hi! I want to know how you made this boxplot, I saw the script that you used for that but a could...

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