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734 results • Page 2 of 15
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Tool: shinyCircos-V2.0: leveraging the creation of Circos plot with enhanced usability and advanced features
shinyCircos visualization Circular Circos genome
12 months ago by Andrewoods ▴ 110
362
votes
82
replies
144k
views
35 follow
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel next-gen ngs
updated 6 weeks 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 13 months ago by 43k • written 13 months ago by ▴ 10
0
votes
1
reply
438
views
Tool: TRcaller : a novel Tool for SSR /STR/TR genotyping from NGS data for short and long reads
SSR NGS genotype STR
updated 13 months ago by 43k • written 13 months ago by • 0
46
votes
9
replies
43k
views
7 follow
Tool: Tools to merge overlapping paired-end reads
ngs Assembly fastq
updated 13 months ago by ▴ 50 • written 7.4 years ago by ★ 1.2k
4
votes
0
replies
896
views
Tool: PyComplexHeatmap: a Python package to visualize multimodal genomics data
visualization Python ComplexHeatmap PyComplexHeatmap
29 days ago by Wubin ▴ 40
0
votes
0
replies
362
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
4.6k
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
816
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
685
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
446
views
Tool: FungiExpresZ: an intuitive package for fungal gene expression data analysis, visualization and discovery
r gene-expression RNA-seq fungi
updated 14 months ago by 43k • written 14 months ago by ★ 2.0k
0
votes
0
replies
485
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
448
views
Tool: HaploCart: Human mtDNA Haplogroup Classification Using a Pangenomic Reference Graph
graph human pangenome haplogroup mitochondrion
15 months ago by Gabriel R. ★ 2.9k
5
votes
0
replies
756
views
Tool: BAM index visualizer - a tool for helping to understand the BAI file format
bam
15 months ago by cmdcolin ★ 3.8k
9
votes
22
replies
9.7k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
10 months ago by vytarasov ▴ 180
2
votes
0
replies
462
views
Tool: GeneWarrior is now open source
open source
16 months ago by r.follador ▴ 90
0
votes
0
replies
612
views
Tool: split pooled paired-end fastq using fqkit
fastq split barcode
updated 16 months ago by 142k • written 16 months ago by ▴ 120
1
vote
0
replies
783
views
Tool: Mabs, a parameter optimizer for Hifiasm and Flye
assembly
7 months ago by shelkmike ★ 1.2k
1
vote
2
replies
715
views
Tool: UUIDtoBarcode Renaming of Folders
UUIDtoBarcode R
updated 17 months ago by ★ 1.2k • written 17 months ago by ▴ 10
4
votes
0
replies
549
views
Tool: Visual analysis of VCF files
vcf visual-analysis
updated 17 months ago by 43k • written 17 months ago by ▴ 270
1
vote
0
replies
455
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 6 months ago by ▴ 10 • written 17 months ago by ▴ 840
4
votes
2
replies
2.7k
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
1.3k
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
1
vote
1
reply
531
views
Tool: trackBrowser: Visualization of sequencing data within a given genome region
RNA browser modification
updated 18 months ago by 35k • written 18 months ago by ▴ 860
3
votes
1
reply
862
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
732
views
Tool: Rethinking containers for cloud native pipelines
workflow container pipeline nextflow
18 months ago by Marcel Ribeiro-Dantas ▴ 470
2
votes
0
replies
841
views
Tool: Query and annotate variants with gnomAD python
sql disease variants python gnomad
18 months ago by Kalin ▴ 50
0
votes
0
replies
350
views
Tool: Binding free energy
Binding-free-energy MD-simulation
updated 16 months ago by 43k • written 19 months ago by • 0
26
votes
22
replies
14k
views
10 follow
Tool: BBSketch - A Tool for Rapid Sequence Comparison
minhash sketch bbmap blast
updated 11 months ago by 43k • written 7.3 years ago by 20k
1
vote
2
replies
637
views
Tool: Easy phylogenomics by BuscoPhylo
Phylogenomics
20 months ago by slimane.khayi ▴ 80
0
votes
0
replies
559
views
Tool: CZ CELLxGENE - Single-cell visualization and analysis tool
visualization scRNA-seq rna-seq
updated 11 months ago by 43k • written 21 months ago by ▴ 40
2
votes
1
reply
667
views
Tool: Best-practice bulk RNA-seq workflow with citations
rnaseq sequencing bulkrnaseq rna
updated 21 months ago by ▴ 30 • written 21 months ago by ▴ 20
2
votes
0
replies
486
views
Tool: NCBI's BLAST ClusteredNR database results have in-cluster analysis
BLAST NCBI ClustereedNR
22 months ago by PeterC_NCBI ▴ 410
1
vote
0
replies
482
views
Tool: Briefings in Bioinformatics: Hiplot visualization toolkit
data-mining visualization
updated 22 months ago by 43k • written 22 months ago by ▴ 10
2
votes
1
reply
738
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 ▴ 770 • written 22 months ago by ▴ 410
2
votes
5
replies
980
views
Tool: Latest release of NCBI Magic-BLAST now available
BLAST NCBI Magic-BLAST
updated 22 months ago by 142k • written 22 months ago by ▴ 410
4
votes
0
replies
683
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
888
views
Tool: Roakvar: do genomic variant analyses with R
oakvar genomics roakvar variant analysis
23 months ago by Ryangguk Kim ▴ 90
3
votes
1
reply
971
views
Tool: OakVar: genomic variant analysis tool
genomics variant
updated 17 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
449
views
Tool: BIRCH Bioinformatics System v3.86
genomics sequence blast transcriptomics
23 months ago by brian.fristensky ▴ 460
1
vote
4
replies
826
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
8.2k
views
10 follow
Tool: pathfindR - Enrichment Analysis using Active Subnetworks
subnetwork R pathway-enrichment
updated 10 months ago by 43k • written 6.2 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
0
votes
0
replies
422
views
Tool: Announcing the Papilloma Virus Episteme (PaVE) 2.0 Release
genomics HPV 3D
2.1 years ago by karlynn.noble ▴ 60
0
votes
0
replies
397
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
2.1 years ago by bigmawen ▴ 430
734 results • Page 2 of 15
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Comment: Can I readmap short reads to rDNA references?
Answer: EdgeR - relationship between logFC and coefficients
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Answer: Server or aws cloud- which one is better for gatk pipeline
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Comment: Can I readmap short reads to rDNA references? by aniigodwinn • 0
Still on this, the reads are from org a, org b, and environmental contaminants. I have a fairly good idea what org b might be but i need to…
Comment: fastq screen aligner no specified. by Ximena • 0
Thank u so much, my OS is linux. I will try your advice.
Comment: In IGV is this a heterogeneous mutation or false call? by Tuck898 • 0
No worries, I can completely appreciate that. I am having investigations similar to a condition causes by the RYR2 gene and was wondering i…
Comment: In IGV is this a heterogeneous mutation or false call? by Pierre Lindenbaum 161k
> RYR1 underneath although I was originally looking at the RYR2 gene. Sorry to sound stupid but does this make sense to what I've previousl…
Comment: In IGV is this a heterogeneous mutation or false call? by Tuck898 • 0
When click the blat it brings me to chr19 and mentions the RYR1 underneath although I was originally looking at the RYR2 gene. Sorry to sou…
Comment: In IGV is this a heterogeneous mutation or false call? by Tuck898 • 0
Thanks for that! I'll try and have a look and see what is amiss if I can... In your opinion what do you feel is wrong in my alignment from…
Comment: In IGV is this a heterogeneous mutation or false call? by Pierre Lindenbaum 161k
yeah.. look at that, there is something wrong in your alignment, many reads were mapped in a location but they are all clipped, so somethin…
Comment: Custom Reference panel creation for data imputation from .vcf files by analyst ▴ 50
Hi [Kevin][1]! I have 80 samples of GBS data. I have called variants through GATK pipeline. Now I have to perform imputation. Do I need …
Comment: In IGV is this a heterogeneous mutation or false call? by Tuck898 • 0
Ah I've just found 'show soft clipped bases' and this is what comes up... how come it is all greyed out? ![enter image description here][…
Comment: In IGV is this a heterogeneous mutation or false call? by Tuck898 • 0
I've just displayed clipped bases and this is what it shows. Does this look right? ![enter image description here][1] ![enter imag…
Comment: In IGV is this a heterogeneous mutation or false call? by Tuck898 • 0
Hi, I really appreciate you taking the time to reply. I'm still learning with IGV and sorry to sound very inexperienced but how would I che…
Answer: In IGV is this a heterogeneous mutation or false call? by Pierre Lindenbaum 161k
there is a clear shift in the depth just close to this mutation, you should set IGV to display the clipped bases + check if there is a DUP …
Comment: Too many unpaired forward reads found by Trimmomatic by SilhouetteQ • 0
Using fastp, I found that the adapter sequence for the forward read is corresponding to Trans2_rc in the NexteraPE-PE.fa, while for the re…
Comment: cellranger error message by Max • 0
I think the problem is your fastq_id. This should also read "RabhiN_PHLGEX". Hope this helps!
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK by Giulio Genovese ▴ 390
@yokofakun is correct. Also, do notice that the GATK option `--RECOVER_SWAPPED_REF_ALT True` does not work with indels. In general, if your…
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