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517 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 7 weeks ago by ▴ 290 • written 11.3 years ago by ★ 4.4k
4
votes
0
replies
916
views
Tool: PyComplexHeatmap: a Python package to visualize multimodal genomics data
visualization Python ComplexHeatmap PyComplexHeatmap
5 weeks ago by Wubin ▴ 40
9
votes
23
replies
9.8k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
5 days ago by vytarasov ▴ 180
1
vote
0
replies
785
views
Tool: Mabs, a parameter optimizer for Hifiasm and Flye
assembly
8 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 6 months ago by ▴ 10 • written 18 months ago by ▴ 840
4
votes
2
replies
1.3k
views
Tool: Introducing Cramino: a *fast* QC tool for long reads
long-read nanopore pacbio
updated 5 weeks ago by 43k • written 18 months ago by 47k
26
votes
22
replies
14k
views
10 follow
Tool: BBSketch - A Tool for Rapid Sequence Comparison
minhash sketch bbmap blast
updated 12 months ago by 43k • written 7.3 years ago by 20k
0
votes
0
replies
561
views
Tool: CZ CELLxGENE - Single-cell visualization and analysis tool
visualization scRNA-seq rna-seq
updated 12 months ago by 43k • written 21 months ago by ▴ 40
28
votes
4
replies
15k
views
Tool: Plotting GSEA output in R
RNA-Seq javaGSEA GSEA
updated 11 months ago by 43k • written 7.8 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 11 months ago by 43k • written 6.2 years ago by ★ 1.3k
16
votes
3
replies
11k
views
Tool: Vcflib Documentation
vcf
updated 11 months ago by 43k • written 11.2 years ago by ★ 2.4k
38
votes
21
replies
19k
views
8 follow
Tool: pybam - 100% python BAM reader
python htspython bam pysam
updated 11 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 11 months ago by 43k • written 6.9 years ago by ★ 3.4k
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
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
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 6.3 years ago by ▴ 150
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
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
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
3
votes
5
replies
2.8k
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
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 10.7 years ago by ▴ 450
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
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
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
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
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
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
2
votes
0
replies
861
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
672
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
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
517 results • Page 2 of 11
Recent Votes
Answer: Generating consensus sequence from bam file
Answer: Short Read Data Genome Assembly
Comment: API kegg - IndexError: list index out of range
Comment: How does FindNeighbors() and FindClusters() related and work?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
lncRNA and ncPEPs identification
Answer: Identifying common DEGs among multiple datasets
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Popular Question to ashkan ▴ 160
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Recent Replies
Answer: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
Comment: Merge clusters in Seurat UMAP by kilcdincer ▴ 10
It did not help either. But I got the answer [here][1] Thank you! [1]: https://github.com/satijalab/seurat/issues/8902
Comment: How to generate table_annovar from VCF input? by Pierre Lindenbaum 161k
there is no `--allsample` option in the "usage" screen you're showing. I suspect you're using an old version ?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by egascon • 0
Thank you very much again. I have learned a lot of things.
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by egascon • 0
It's a microarryay experiment, not RNASeq
Comment: Sam file Header problem by Pierre Lindenbaum 161k
https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences? by DGTool ▴ 20
I have also recently come across another global alignment algorithm that was recently released which could seem pretty interesting to test …
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by b.contreras.moreira ▴ 190
Not sure, you might ask in the repo, please share here the response if you find it
Comment: How to generate table_annovar from VCF input? by LucisTheFather • 0
Would you be more specific to your question? Do you mean how to debug this syntax error?
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
thank you
Comment: How to extract cells of different species after mapping with combined genome? by Tony • 0
I think this method should be applicable to all high-throughput single-cell RNA-seq platforms. Although the method of determining cell spec…
Comment: BiomartException: Query ERROR for existing dataset in BioMart by Nyksubuz ▴ 20
The dataset you want (taestivum_eg_gene) exists within the "plants_mart" schema, not the default schema. Your current code assumes the defa…
Comment: Add line under stat test by Nyksubuz ▴ 20
You could use [this][1] [1]: https://ggplot2.tidyverse.org/reference/geom_segment.html
Comment: API kegg - IndexError: list index out of range by Nyksubuz ▴ 20
It might be because the gene symbol is not found in the KEGG database. Add some extra error handling before parsing the results or do a man…
Comment: Sam file Header problem by saifulislam99121 • 0
Thank you for your reply. I am not very much sure about this RG. Can you explain me a bit?
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