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521 results • Page 2 of 11
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362
votes
82
replies
144k
views
35 follow
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel next-gen ngs
updated 5 weeks ago by ▴ 290 • written 11.2 years ago by ★ 4.4k
4
votes
0
replies
876
views
Tool: PyComplexHeatmap: a Python package to visualize multimodal genomics data
visualization Python ComplexHeatmap PyComplexHeatmap
21 days ago by Wubin ▴ 40
9
votes
22
replies
9.7k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
9 months ago by vytarasov ▴ 180
1
vote
0
replies
778
views
Tool: Mabs, a parameter optimizer for Hifiasm and Flye
assembly
7 months ago by shelkmike ★ 1.2k
2
votes
4
replies
1.0k
views
Tool: Tool: Quick Command To Change BED file Naming Convention
bed awk
updated 5 months ago by ▴ 10 • written 17 months ago by ▴ 840
4
votes
2
replies
1.2k
views
Tool: Introducing Cramino: a *fast* QC tool for long reads
long-read nanopore pacbio
updated 26 days ago by 43k • written 18 months ago by 47k
26
votes
22
replies
13k
views
10 follow
Tool: BBSketch - A Tool for Rapid Sequence Comparison
minhash sketch bbmap blast
updated 11 months ago by 43k • written 7.2 years ago by 20k
0
votes
0
replies
557
views
Tool: CZ CELLxGENE - Single-cell visualization and analysis tool
visualization scRNA-seq rna-seq
updated 11 months ago by 43k • written 20 months ago by ▴ 40
28
votes
4
replies
15k
views
Tool: Plotting GSEA output in R
RNA-Seq javaGSEA GSEA
updated 10 months ago by 43k • written 7.7 years ago by ▴ 850
25
votes
19
replies
8.2k
views
10 follow
Tool: pathfindR - Enrichment Analysis using Active Subnetworks
subnetwork R pathway-enrichment
updated 10 months ago by 43k • written 6.1 years ago by ★ 1.3k
16
votes
3
replies
11k
views
Tool: Vcflib Documentation
vcf
updated 10 months ago by 43k • written 11.1 years ago by ★ 2.4k
38
votes
21
replies
19k
views
8 follow
Tool: pybam - 100% python BAM reader
python htspython bam pysam
updated 10 months ago by 43k • written 8.1 years ago by 13k
76
votes
14
replies
13k
views
10 follow
Tool: karyoploteR: uncircle your genomes
karyoploteR Rdataviz NGS
updated 10 months ago by 43k • written 6.9 years ago by ★ 3.4k
2
votes
0
replies
591
views
Tool: Introducing ElasticBLAST – Run bigger BLAST searches faster on the Cloud
ElasticBLAST BLAST NCBI
updated 10 months ago by 43k • written 2.1 years ago by ▴ 410
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 10 months ago by 43k • written 11.2 years ago by 19k
5
votes
2
replies
2.4k
views
Tool: eLabFTW: a free and open source electronic lab notebook
elabftw free-open-source-software php
updated 10 months ago by 43k • written 4.6 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 10 months ago by 43k • written 5.9 years ago by ▴ 50
2
votes
6
replies
3.4k
views
Tool: microbiomeMarker: microbiome biomarker analysis in R
stamp microbiome lefse
updated 10 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 10 months ago by 43k • written 4.7 years ago by ★ 3.6k
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 10 months ago by 43k • written 6.2 years ago by ▴ 150
28
votes
17
replies
5.1k
views
7 follow
Tool: PCAtools: everything Principal Components Analysis
eigenvector pca bioconductor R
updated 10 months ago by 43k • written 5.2 years ago by 87k
10
votes
5
replies
2.4k
views
Tool: Genozip: A new compression tool for FASTQ, BAM, VCF and more
bam vcf fastq compression
10 months ago by Divon ▴ 230
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 10 months ago by 43k • written 3.2 years ago by ▴ 430
3
votes
5
replies
2.7k
views
Tool: Extend 3' UTR of a GTF file
annotation python RNA-Seq GTF
updated 10 months ago by 43k • written 3.6 years ago by ★ 1.4k
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 10 months ago by 43k • written 10.6 years ago by ▴ 450
21
votes
14
replies
9.4k
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 10 months ago by 43k • written 3.4 years ago by ★ 3.2k
9
votes
7
replies
2.9k
views
Tool: DiffBind 3.0: Extensive updates in Bioconductor 3.12
DiffBind ChIP-Seq diffbind ATAC-seq chipseq
updated 10 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 10 months ago by 43k • written 4.5 years ago by ▴ 380
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 11 weeks ago by • 0 • written 7.0 years ago by 3.5k
1
vote
0
replies
596
views
Tool: Super easy to use free paper retrieval artifact: PyPubMed
python pubmed software
updated 10 months ago by 43k • written 2.9 years ago by ▴ 420
0
votes
0
replies
697
views
Tool: IPC 2.0: prediction of isoelectric point and pKa dissociation constants
deep-learning isoelectric-point 2D-PAGE pKa
updated 10 months ago by 43k • written 2.9 years ago by • 0
8
votes
6
replies
5.8k
views
Tool: chromoMap- R package for Interactive visualization and Annotation of chromosomes or regions of any living organism.
annotation R genome visualization
updated 10 months ago by 43k • written 5.0 years ago by ▴ 80
13
votes
14
replies
6.1k
views
9 follow
Tool: open-cravat: variant annotation tool
open-cravat
updated 10 months ago by 43k • written 5.4 years ago by ▴ 260
2
votes
1
reply
773
views
Tool: Bioinformatics Programming Package
Package
updated 10 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 141k • written 5.2 years ago by ★ 1.4k
2
votes
0
replies
856
views
Tool: New location tracking tool for SARS-CoV-2 variant surveillance
sars-cov-2 variant covid-19
updated 10 months ago by 43k • written 3.1 years ago by ▴ 20
12
votes
5
replies
6.1k
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 11 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 10 months ago by 43k • written 3.2 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 10 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 10 months ago by 43k • written 3.7 years ago by 87k
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 10 months ago by 43k • written 3.2 years ago by ▴ 450
0
votes
0
replies
667
views
Tool: MultiLink Analysis: Brain Network Comparison via Sparse Connectivity Analysis
networks neuroscience connectome brain
updated 10 months ago by 43k • written 3.2 years ago by • 0
1
vote
0
replies
679
views
Tool: BiOkeanos - the largest(*) biomedical database catalogue and discovery tool
database catalogue data
updated 10 months ago by 43k • written 3.2 years ago by ▴ 20
0
votes
0
replies
836
views
Tool: Analyze & Visualize Nephele Microbiome Results Using MicrobiomeDB
microbiome sequence
updated 10 months ago by 43k • written 3.2 years ago by ▴ 60
22
votes
20
replies
4.8k
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 10 months ago by 43k • written 5.5 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 10 months ago by 43k • written 3.6 years ago by 8.6k
0
votes
0
replies
629
views
Tool: Cytoscape Network analysis
software-error cytoscape
updated 10 months ago by 43k • written 3.2 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 10 months ago by 43k • written 3.3 years ago by • 0
11
votes
2
replies
7.0k
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 10 months ago by 43k • written 5.8 years ago by ★ 2.5k
521 results • Page 2 of 11
Recent Votes
Comment: Can't install AnnotationHub
C: TOPGO- how to do GO enrichment using a custom go database?
Answer: NGS forensics: how to know if data is fabricated
Comment: Adjust pvalue in R with different approach give me all different outcome
Comment: Bacterial plasmid analysis
Comment: DESeq2 processing problems
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
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Popular Question to mgranada3 ▴ 30
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Recent Replies
Answer: Basic stats in hierfstat by mdav • 0
Hi Zoe, did you find an answer for this? I am also getting the same error.
Comment: GATK won't produce figures while analyzing covariates to generate 'recal_plots.p by GenoMax 141k
Your cluster may be missing libraries etc to create the PDF plots (this looks like a cluster job submission) on your cluster. Did you check…
Comment: Post-imputation plot by kl ▴ 10
Ok yes I think my thought was that given these errors, I could remove the mismatches and flip the alleles which seem to need flipping based…
Comment: Bacterial plasmid analysis by nicole.kavanagh • 0
I think I will perhaps use their predominant PlasmidFinder type to group plasmids together and create separate core phylogenies for each as…
Comment: Bacterial plasmid analysis by GenoMax 141k
Can you classify the plasmids based on function (resistance genes they are carrying or some other criteria). Sizes above are indicating a w…
Comment: DESeq2 processing problems by ATpoint 82k
Initially posted here https://support.bioconductor.org/p/9158036/ where I suggested to put code and data and noted that GEOquery returns ar…
Answer: Post-imputation plot by LChart 3.9k
I agree that some need to be flipped (A/T and C/G where your panel frequency is 1 - ref panel frequency). There are other variants which yo…
Comment: RNA editing sites based on DNA seq and RNA seq by Adam ▴ 30
Are those 20% unaligned reads coming after hyper-editing detection?
Answer: How to find overlap of clusters in two seurat porject by Adam ▴ 30
I think your best bet would be to use annotation mapping. You can use the features of your clusters in group 1 and apply them to group 2 to…
Answer: DESeq2 processing problems by Adam ▴ 30
> when I put in the dataset, I am not able to run it for DEG analysis because system asks me to remove the first column which is of gene na…
Comment: Bacterial plasmid analysis by nicole.kavanagh • 0
Thank you so much for your quick response, I have been searching scientific papers for about a week but have failed to come up with a reaso…
Comment: Bacterial plasmid analysis by GenoMax 141k
> however I'm not sure this would be appropriate in my case as the plasmid sequences are obviously much more diverse and vary in size Can…
Answer: cnetplot category names are too long by bkleiboeker ▴ 370
I'm sure someone could find a more elegant solution using `stringr::str_wrap`, but for a one-time solution I did this: # my results of…
Comment: Telescope issue by GenoMax 141k
You could edit the SAM file but I wonder if this problem is present in your original fastq data file so if not inconvenient do the alignmen…
Comment: Mutect2 for mitochondria variant discovery by GenoMax 141k
> I keep getting error. Without providing information about the actual error no one can help. Please edit the post and add this informati…
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