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737 results • Page 2 of 15
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505
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Tool: Easy API For Running Bioinformatics Jobs Via Python In The Cloud
api execution
12 months ago by Sasha ▴ 850
0
votes
0
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489
views
Tool: Single-cell RNA-seq data analysis tool Cellenics®
single-cell RNA-seq scRNA-seq
updated 12 months ago by 44k • written 12 months ago by • 0
0
votes
1
reply
999
views
Tool: web app for user-friendly analysis of 16S rRNA gene meta-barcoding NGS data - bacterial microbiome
qiime2 16s microbiome ngs
updated 12 months ago by 44k • written 12 months ago by • 0
1
vote
2
replies
883
views
Tool: Tinybio Slackbot - a large language model slackbot for bioinformatics
qa
12 months ago by Sasha ▴ 850
0
votes
0
replies
469
views
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 8 weeks ago by ▴ 290 • written 11.3 years ago by ★ 4.4k
0
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0
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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 44k • written 13 months ago by ▴ 10
0
votes
1
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448
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 44k • 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 7.5 years ago by ★ 1.2k
4
votes
0
replies
931
views
Tool: PyComplexHeatmap: a Python package to visualize multimodal genomics data
visualization Python ComplexHeatmap PyComplexHeatmap
5 weeks ago by Wubin ▴ 40
0
votes
0
replies
367
views
Tool: BioLabImage - Mac program for DNA/RNA/protein gel/blot, cells/colonies image analysis
image-analysis gel blot cells colonies
updated 14 months ago by 44k • written 14 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 14 months ago by 44k • written 8.2 years ago by ▴ 350
2
votes
2
replies
826
views
Tool: NCBI's Foreign Contamination Screen (FCS) tool improves the quality of GenBank submissions
NCBI Submission GenBank
14 months ago by PeterC_NCBI ▴ 410
1
vote
0
replies
692
views
Tool: BioLabDNA - Mac program for DNA analysis and cloning.
cloning DNA protein alignment assembly
14 months ago by vytarasov ▴ 180
1
vote
0
replies
450
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 44k • written 15 months ago by ★ 2.0k
0
votes
0
replies
493
views
Tool: GraphBio: A shiny web app to easily perform popular visualization analysis for omics data
visualization heatmap volcano-plot
updated 15 months ago by 44k • written 15 months ago by • 0
1
vote
0
replies
460
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
772
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
23
replies
9.9k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
10 days ago by vytarasov ▴ 180
2
votes
0
replies
467
views
Tool: GeneWarrior is now open source
open source
16 months ago by r.follador ▴ 90
0
votes
0
replies
617
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
789
views
Tool: Mabs, a parameter optimizer for Hifiasm and Flye
assembly
8 months ago by shelkmike ★ 1.2k
1
vote
2
replies
723
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
558
views
Tool: Visual analysis of VCF files
vcf visual-analysis
updated 17 months ago by 44k • written 17 months ago by ▴ 270
1
vote
0
replies
464
views
Tool: BioIllustrator - Mac program for the creation of illustrations for scientific articles
molecular cell biology scientific illustration
18 months ago by vytarasov ▴ 180
2
votes
4
replies
1.1k
views
Tool: Tool: Quick Command To Change BED file Naming Convention
bed awk
updated 6 months ago by ▴ 10 • written 18 months ago by ▴ 850
4
votes
2
replies
2.7k
views
Tool: pyMSAviz - MSA visualization python package for sequence analysis
visualization MSA Python
updated 18 months ago by ★ 2.0k • written 18 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 6 weeks ago by 44k • written 18 months ago by 47k
1
vote
1
reply
539
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
873
views
Tool: The Encyclopedia of RNA Epitranscriptome : decoding the mechanisms and functions of diverse RNA modifications
m6A m1A m5C modification epitranscriptome
19 months ago by lsp03yjh ▴ 860
4
votes
2
replies
746
views
Tool: Rethinking containers for cloud native pipelines
workflow container pipeline nextflow
19 months ago by Marcel Ribeiro-Dantas ▴ 470
2
votes
0
replies
853
views
Tool: Query and annotate variants with gnomAD python
sql disease variants python gnomad
19 months ago by Kalin ▴ 50
0
votes
0
replies
352
views
Tool: Binding free energy
Binding-free-energy MD-simulation
updated 17 months ago by 44k • 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 12 months ago by 44k • written 7.3 years ago by 20k
1
vote
2
replies
645
views
Tool: Easy phylogenomics by BuscoPhylo
Phylogenomics
20 months ago by slimane.khayi ▴ 80
0
votes
0
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565
views
Tool: CZ CELLxGENE - Single-cell visualization and analysis tool
visualization scRNA-seq rna-seq
updated 12 months ago by 44k • written 21 months ago by ▴ 40
2
votes
1
reply
680
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
489
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
488
views
Tool: Briefings in Bioinformatics: Hiplot visualization toolkit
data-mining visualization
updated 22 months ago by 44k • written 22 months ago by ▴ 10
2
votes
1
reply
741
views
Tool: NCBI IgBLAST release 1.19.0 for immunoglobulin and T cell receptor variable domain sequences now available
BLAST IgBLAST NCBI
updated 23 months ago by ▴ 770 • written 23 months ago by ▴ 410
2
votes
5
replies
987
views
Tool: Latest release of NCBI Magic-BLAST now available
BLAST NCBI Magic-BLAST
updated 22 months ago by 142k • written 23 months ago by ▴ 410
4
votes
0
replies
698
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
23 months ago by Single Cell Portal ▴ 40
1
vote
2
replies
895
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
982
views
Tool: OakVar: genomic variant analysis tool
genomics variant
updated 17 months ago by 44k • written 24 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 24 months ago by ▴ 700 • written 24 months ago by ▴ 450
0
votes
0
replies
452
views
Tool: BIRCH Bioinformatics System v3.86
genomics sequence blast transcriptomics
24 months ago by brian.fristensky ▴ 460
1
vote
4
replies
837
views
Tool: Quick Command to Filter Bam Files
bed awk
24 months ago by Sasha ▴ 850
28
votes
4
replies
15k
views
Tool: Plotting GSEA output in R
RNA-Seq javaGSEA GSEA
updated 11 months ago by 44k • 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 44k • written 6.2 years ago by ★ 1.3k
16
votes
3
replies
11k
views
Tool: Vcflib Documentation
vcf
updated 11 months ago by 44k • written 11.2 years ago by ★ 2.4k
737 results • Page 2 of 15
Recent Votes
Comment: NGS forensics: how to know if data is fabricated
T2T-CHM13 "complete" human genome gff/gtf annotation file
Answer: T2T-CHM13 "complete" human genome gff/gtf annotation file
Comment: Problem in getting geo file through GEOQUERY
Answer: Problem in getting geo file through GEOQUERY
Comment: SnpEff and Snpsift
Comment: Problem in getting geo file through GEOQUERY
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Recent Replies
Comment: BiomartException: Query ERROR for existing dataset in BioMart by Nyksubuz ▴ 20
Could share some examples for gene_ids?
Comment: Problem in getting geo file through GEOQUERY by anasjamshed ▴ 120
yeah but i am unable to find the link of GPL6244.soft.gz
Comment: Problem in getting geo file through GEOQUERY by ATpoint 82k
> Can you send me ftp link so I can download that soft file manually? Please find this link on your own by browsing the respective GEO ent…
Comment: Problem in getting geo file through GEOQUERY by anasjamshed ▴ 120
Thanks . I have downloaded all other files but just have problem in Error in downloadFile(myurl, destfile, mode = mode, quiet = TRUE)…
Answer: Problem in getting geo file through GEOQUERY by ATpoint 82k
Code runs for me and finishes in seconds. Maybe some poor internet connection on your end. Just set the timeout to 9999999 and retry. If th…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c by ezz3 • 0
Thanks. I was wondering if that is the case but was having some issues understanding the transanno code which is written in rust and I don…
Answer: Multi-ploid data in ANGSD and NGSadmix by andersdetermig ▴ 20
1 ) I would not expect the haploid individuals to always cluster together but the model assumptions are violated. First of all the diploid…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c by Pierre Lindenbaum 161k
"Are you using correct reference?" may be your reference is not using the same chrM. see https://www.biostars.org/p/199796/#199803
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument by shpak.max ▴ 50
Could you please elaborate on what you mean by passing -L or -V, i.e. what would the appropriate argument be for -L with UnifiedGenotyper f…
Answer: Add stats to the plot by Ghada • 0
It works. I have added this code my_comparisons=list(c("HRSV", "HRSV_RBV")) plot + stat_compare_means(method = "wilcox.test",comparis…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument by LChart 3.9k
I believe UnifiedGenotyper is a locus walker that sets `emitEmptySites() = False`. As such you will not see entries for positions that have…
Comment: Problem in getting geo file through GEOQUERY by anasjamshed ▴ 120
Basically this is my code: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # # pkgs <- rowna…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument by shpak.max ▴ 50
If that were the case, I would expect there not to be any uncalled sites in the vcf, yet there are a large number of sites with "." placeho…
Comment: Problem in getting geo file through GEOQUERY by bk11 ★ 2.5k
It just runs fine for me with just a single line of code. library(GEOquery) GSE1145 <- getGEO("GSE1145", GSEMatrix=TRUE) …
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument by Dave Carlson ★ 1.7k
I can't speak to UnifiedGenotyper, as it has been many years since GATK stopped supporting it, and I have not used it in a long time. But …
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