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733 results • Page 2 of 15
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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 27 days ago by ▴ 290 • written 11.2 years ago by ★ 4.4k
0
votes
0
replies
3.3k
views
Tool: euka: Robust detection of eukaryotic taxa from modern and ancient environmental DNA using pangenomic reference graphs.
pangenomics vg sedaDNA graph environmental-DNA
updated 12 months ago by 43k • written 12 months ago by ▴ 10
0
votes
1
reply
428
views
Tool: TRcaller : a novel Tool for SSR /STR/TR genotyping from NGS data for short and long reads
SSR NGS genotype STR
updated 12 months ago by 43k • written 12 months ago by • 0
46
votes
9
replies
43k
views
7 follow
Tool: Tools to merge overlapping paired-end reads
ngs Assembly fastq
updated 12 months ago by ▴ 50 • written 7.4 years ago by ★ 1.2k
4
votes
0
replies
860
views
Tool: PyComplexHeatmap: a Python package to visualize multimodal genomics data
visualization Python ComplexHeatmap PyComplexHeatmap
12 days ago by Wubin ▴ 40
0
votes
0
replies
354
views
Tool: BioLabImage - Mac program for DNA/RNA/protein gel/blot, cells/colonies image analysis
image-analysis gel blot cells colonies
updated 13 months ago by 43k • written 13 months ago by ▴ 180
6
votes
10
replies
4.5k
views
Tool: Giant Virus Finder - discover giant virus sequences in metagenomes
Giant-Virus-Finder
updated 13 months ago by 43k • written 8.2 years ago by ▴ 350
2
votes
2
replies
794
views
Tool: NCBI's Foreign Contamination Screen (FCS) tool improves the quality of GenBank submissions
NCBI Submission GenBank
13 months ago by PeterC_NCBI ▴ 410
1
vote
0
replies
668
views
Tool: BioLabDNA - Mac program for DNA analysis and cloning.
cloning DNA protein alignment assembly
13 months ago by vytarasov ▴ 180
1
vote
0
replies
427
views
Tool: FungiExpresZ: an intuitive package for fungal gene expression data analysis, visualization and discovery
r gene-expression RNA-seq fungi
updated 13 months ago by 43k • written 14 months ago by ★ 2.0k
0
votes
0
replies
470
views
Tool: GraphBio: A shiny web app to easily perform popular visualization analysis for omics data
visualization heatmap volcano-plot
updated 14 months ago by 43k • written 14 months ago by • 0
1
vote
0
replies
439
views
Tool: HaploCart: Human mtDNA Haplogroup Classification Using a Pangenomic Reference Graph
graph human pangenome haplogroup mitochondrion
14 months ago by Gabriel R. ★ 2.9k
5
votes
0
replies
728
views
Tool: BAM index visualizer - a tool for helping to understand the BAI file format
bam
14 months ago by cmdcolin ★ 3.8k
9
votes
22
replies
9.7k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
9 months ago by vytarasov ▴ 180
2
votes
0
replies
453
views
Tool: GeneWarrior is now open source
open source
15 months ago by r.follador ▴ 90
0
votes
0
replies
598
views
Tool: split pooled paired-end fastq using fqkit
fastq split barcode
updated 15 months ago by 141k • written 15 months ago by ▴ 120
1
vote
0
replies
769
views
Tool: Mabs, a parameter optimizer for Hifiasm and Flye
assembly
7 months ago by shelkmike ★ 1.2k
1
vote
2
replies
706
views
Tool: UUIDtoBarcode Renaming of Folders
UUIDtoBarcode R
updated 16 months ago by ★ 1.2k • written 16 months ago by ▴ 10
4
votes
0
replies
529
views
Tool: Visual analysis of VCF files
vcf visual-analysis
updated 16 months ago by 43k • written 16 months ago by ▴ 270
1
vote
0
replies
442
views
Tool: BioIllustrator - Mac program for the creation of illustrations for scientific articles
molecular cell biology scientific illustration
17 months ago by vytarasov ▴ 180
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
2.6k
views
Tool: pyMSAviz - MSA visualization python package for sequence analysis
visualization MSA Python
updated 17 months ago by ★ 2.0k • written 17 months ago by ▴ 150
4
votes
2
replies
1.2k
views
Tool: Introducing Cramino: a *fast* QC tool for long reads
long-read nanopore pacbio
updated 17 days ago by 43k • written 17 months ago by 47k
1
vote
1
reply
522
views
Tool: trackBrowser: Visualization of sequencing data within a given genome region
RNA browser modification
updated 17 months ago by 35k • written 17 months ago by ▴ 860
3
votes
1
reply
847
views
Tool: The Encyclopedia of RNA Epitranscriptome : decoding the mechanisms and functions of diverse RNA modifications
m6A m1A m5C modification epitranscriptome
18 months ago by lsp03yjh ▴ 860
4
votes
2
replies
710
views
Tool: Rethinking containers for cloud native pipelines
workflow container pipeline nextflow
18 months ago by Marcel Ribeiro-Dantas ▴ 470
2
votes
0
replies
824
views
Tool: Query and annotate variants with gnomAD python
sql disease variants python gnomad
18 months ago by Kalin ▴ 50
0
votes
0
replies
342
views
Tool: Binding free energy
Binding-free-energy MD-simulation
updated 16 months ago by 43k • written 18 months ago by • 0
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
1
vote
2
replies
621
views
Tool: Easy phylogenomics by BuscoPhylo
Phylogenomics
19 months ago by slimane.khayi ▴ 80
0
votes
0
replies
554
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
2
votes
1
reply
641
views
Tool: Best-practice bulk RNA-seq workflow with citations
rnaseq sequencing bulkrnaseq rna
updated 20 months ago by ▴ 30 • written 20 months ago by ▴ 20
2
votes
0
replies
474
views
Tool: NCBI's BLAST ClusteredNR database results have in-cluster analysis
BLAST NCBI ClustereedNR
21 months ago by PeterC_NCBI ▴ 410
1
vote
0
replies
476
views
Tool: Briefings in Bioinformatics: Hiplot visualization toolkit
data-mining visualization
updated 21 months ago by 43k • written 21 months ago by ▴ 10
2
votes
1
reply
723
views
Tool: NCBI IgBLAST release 1.19.0 for immunoglobulin and T cell receptor variable domain sequences now available
BLAST IgBLAST NCBI
updated 22 months ago by ▴ 740 • written 22 months ago by ▴ 410
2
votes
5
replies
950
views
Tool: Latest release of NCBI Magic-BLAST now available
BLAST NCBI Magic-BLAST
updated 21 months ago by 141k • written 22 months ago by ▴ 410
4
votes
0
replies
672
views
Tool: Single Cell Portal - a free and open platform for viewing, sharing and interacting with single cell genomic data
gene-expression scrna-seq single-cell visualization
22 months ago by Single Cell Portal ▴ 40
1
vote
2
replies
874
views
Tool: Roakvar: do genomic variant analyses with R
oakvar genomics roakvar variant analysis
22 months ago by Ryangguk Kim ▴ 90
3
votes
1
reply
958
views
Tool: OakVar: genomic variant analysis tool
genomics variant
updated 16 months ago by 43k • written 23 months ago by ▴ 90
27
votes
5
replies
1.9k
views
6 follow
Tool: Efficient querying of genomic reference databases with gget
ensembl enrichr ncbi gget uniprot
updated 23 months ago by ▴ 700 • written 23 months ago by ▴ 450
0
votes
0
replies
436
views
Tool: BIRCH Bioinformatics System v3.86
genomics sequence blast transcriptomics
23 months ago by brian.fristensky ▴ 460
1
vote
4
replies
807
views
Tool: Quick Command to Filter Bam Files
bed awk
23 months ago by Sasha ▴ 840
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
8.1k
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 8.0 years ago by 13k
76
votes
14
replies
12k
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
0
votes
0
replies
413
views
Tool: Announcing the Papilloma Virus Episteme (PaVE) 2.0 Release
genomics HPV 3D
2.0 years ago by karlynn.noble ▴ 60
0
votes
0
replies
387
views
Tool: Nature Communications: New AI tool for in-depth cleaning of a wide range of noise in single-cell RNA-Seq data
denoise scRNA-Seq AutoClass AI
2.0 years ago by bigmawen ▴ 430
9
votes
7
replies
1.7k
views
Tool: miniDBG - a Jupyter notebook for teaching De Bruijn Graph assembly
python deBruijnGraph de_bruijn_graph assembly teaching
24 months ago by Michael 54k
733 results • Page 2 of 15
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Comment: Intersect multiple BED files
Exciting 2024 Summer Internship Opportunity in Translational Genetics Arrowhead Pharmaceuticals!
Comment: Correlation for ATAC-Seq and Chip-Seq
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
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Recent Replies
Answer: How to compare the quality of assemblies by colindaven 6.4k
Are you sure you have looked into the HiFiasm output files (fasta and GFA) in detail and excluded non-primary contigs, hap1, hap2 and other…
Answer: How to identify gaps in a genome? by colindaven 6.4k
You can use seqtk to find gaps in a fasta https://github.com/lh3/seqtk seqtk gap Usage: seqtk gap [-l 50] <in.fa>
Comment: some error in building kraken2 database by GenoMax 141k
> Obviously, running kraken2 after the build is complete does not produce the correct results What do you get instead? Error/no output? Ha…
Comment: Failed kmer content by GenoMax 141k
Can you post a screenshot of what you are referring to? Why did you choose to "clean" your data? FastQC analysis needs to be done keeping…
Comment: Help for coding: Trinity for differential gene expression studies by rhossen • 0
It should be great if I have any assistance in my build up command using trinity package...
Comment: Filter BAM to keep only alignments at an interval, ignoring reads spliced over by WouterDeCoster 47k
I want reads in a specific short interval, but if I do that with samtools view I also get reads that are spliced over that interval.
Answer: Help for coding: Trinity for differential gene expression studies by mchour • 0
Hello, I would recommend following RSEM wiki for more information about the options, or even run RSEM directly, not with the script provi…
Answer: WGCNA preservation analysis by Michael 54k
This seems like a model case for why we need better sustainable bioinformatics data and services. I don't know the exact background behind …
Comment: some error in building kraken2 database by Art1ess • 0
this is names.dmp:![names.dmp][1] and nodes.dmp![nodes.dmp][2] [1]: /media/images/33cc9a8b-4818-48b4-913d-1c2b2185 [2]: /media/i…
Comment: Filter BAM to keep only alignments at an interval, ignoring reads spliced over by Pierre Lindenbaum 161k
see also : https://www.biostars.org/p/9537698/ ; https://www.biostars.org/p/9464312/ ; https://www.biostars.org/p/417123/
Comment: Filter BAM to keep only alignments at an interval, ignoring reads spliced over by Pierre Lindenbaum 161k
what's the gray section ? it's the read you want ? do you only want the reads that end at the splice event (single point location) ?
Comment: interpretartion of a vcf file by Pierre Lindenbaum 161k
yes if there is more than one sample genotyped.
Comment: interpretartion of a vcf file by samuelkalandarov2002 ▴ 10
Is it typical to observe such a profile in the context of diploid organism ?
Answer: Plots for DNA methylation data by Basti ★ 2.0k
Yes you can use ggplot2 to create your own plots from a table of results from a differential methylation analysis. You just need to adapt a…
Comment: Heatmap and rna-seq by Basti ★ 2.0k
This forum is not dedicated to this type of request, there are many online tutorials for creating heatmaps accessible with simple internet …
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