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738 results • Page 2 of 15
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5
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3
replies
886
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Tool: Experiment Generator
gpt
updated 11 months ago by 4.2k • written 11 months ago by ▴ 850
0
votes
0
replies
509
views
Tool: Easy API For Running Bioinformatics Jobs Via Python In The Cloud
api execution
12 months ago by Sasha ▴ 850
0
votes
0
replies
493
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
1000
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
890
views
Tool: Tinybio Slackbot - a large language model slackbot for bioinformatics
qa
12 months ago by Sasha ▴ 850
0
votes
0
replies
471
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
145k
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
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 44k • written 13 months ago by ▴ 10
0
votes
1
reply
451
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
943
views
Tool: PyComplexHeatmap: a Python package to visualize multimodal genomics data
visualization Python ComplexHeatmap PyComplexHeatmap
6 weeks ago by Wubin ▴ 40
0
votes
0
replies
370
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 8.3 years ago by ▴ 350
2
votes
2
replies
830
views
Tool: NCBI's Foreign Contamination Screen (FCS) tool improves the quality of GenBank submissions
NCBI Submission GenBank
14 months ago by PeterC_NCBI ▴ 420
1
vote
0
replies
697
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
451
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
494
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
464
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
780
views
Tool: BAM index visualizer - a tool for helping to understand the BAI file format
bam
16 months ago by cmdcolin ★ 3.8k
9
votes
23
replies
9.9k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
15 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
618
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
791
views
Tool: Mabs, a parameter optimizer for Hifiasm and Flye
assembly
8 months ago by shelkmike ★ 1.2k
1
vote
2
replies
726
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
559
views
Tool: Visual analysis of VCF files
vcf visual-analysis
updated 18 months ago by 44k • written 18 months ago by ▴ 270
1
vote
0
replies
465
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 7 weeks ago by 44k • written 18 months ago by 47k
1
vote
1
reply
542
views
Tool: trackBrowser: Visualization of sequencing data within a given genome region
RNA browser modification
updated 18 months ago by 35k • written 19 months ago by ▴ 860
3
votes
1
reply
874
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
757
views
Tool: Rethinking containers for cloud native pipelines
workflow container pipeline nextflow
19 months ago by Marcel Ribeiro-Dantas ▴ 470
2
votes
0
replies
857
views
Tool: Query and annotate variants with gnomAD python
sql disease variants python gnomad
19 months ago by Kalin ▴ 50
0
votes
0
replies
354
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
648
views
Tool: Easy phylogenomics by BuscoPhylo
Phylogenomics
20 months ago by slimane.khayi ▴ 80
0
votes
0
replies
569
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
689
views
Tool: Best-practice bulk RNA-seq workflow with citations
rnaseq sequencing bulkrnaseq rna
updated 22 months ago by ▴ 30 • written 22 months ago by ▴ 20
2
votes
0
replies
492
views
Tool: NCBI's BLAST ClusteredNR database results have in-cluster analysis
BLAST NCBI ClustereedNR
22 months ago by PeterC_NCBI ▴ 420
1
vote
0
replies
489
views
Tool: Briefings in Bioinformatics: Hiplot visualization toolkit
data-mining visualization
updated 22 months ago by 44k • written 23 months ago by ▴ 10
2
votes
1
reply
749
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 ▴ 420
2
votes
5
replies
991
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 ▴ 420
4
votes
0
replies
700
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
898
views
Tool: Roakvar: do genomic variant analyses with R
oakvar genomics roakvar variant analysis
24 months ago by Ryangguk Kim ▴ 90
3
votes
1
reply
988
views
Tool: OakVar: genomic variant analysis tool
genomics variant
updated 17 months ago by 44k • written 2.0 years 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
455
views
Tool: BIRCH Bioinformatics System v3.86
genomics sequence blast transcriptomics
24 months ago by brian.fristensky ▴ 460
1
vote
4
replies
839
views
Tool: Quick Command to Filter Bam Files
bed awk
2.0 years 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
8.3k
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
738 results • Page 2 of 15
Recent Votes
C: The Biostar Handbook. A bioinformatics e-book for beginners.
Answer: Error with BiocParallel. No barcodes files found
Error with BiocParallel. No barcodes files found
Comment: How do we do quantification using stringtie merge option for all the merged samp
Answer: bcftools view error: the tag "mis" is not defined in the VCF header
Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
Search within posts based on tags using the Biostars API
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Recent Replies
Comment: How do we do quantification using stringtie merge option for all the merged samp by Varsha • 0
Thank you for the detailed explanation.
Answer: How can run cd-hit-est with a clstr threshold less than 0.8? by Asaf 10k
For future reference The 0.8 identity threshold for EST (nucleotides) is hardcoded. However, there's an option to use `-D` (distance) in…
Answer: Tools for chromosomal aneuploidy detection by a.alnawfal.1992 ▴ 260
As far as I know, all the tools utilised control group to compute the z score for chromosomal aneuploidy. but is your goal detect chromosom…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by Sara ▴ 30
I used Seurat, and in Seurat, I have gene names (which some are with gene-symbols and some with ENSG ids). Then I did Pseudobulk. how can …
Comment: How to decrease the motif score? by ATpoint 82k
So you scan the entire genome and got nothing significant? Is that the issue?
Comment: perl Error - needLargeMem Bigwig by b.contreras.moreira ▴ 200
A quick search suggests the problem is your empty input file? See <https://biostar.galaxyproject.org/p/6794>
Comment: Invalid CIGAR after using bam clipOverlap by MboiTui ▴ 20
ooh good pickup. Might not be the problem but definitely not helping. Will re-run with streamlined workflow and with double quotes and see …
Comment: Invalid CIGAR after using bam clipOverlap by Pierre Lindenbaum 162k
may be not the problem but why this ` RG:Z:H7J22DRX3.${lane}-1C23074F ` in the RG. you're using single quotes with bwa-mem and it won't …
Comment: Invalid CIGAR after using bam clipOverlap by MboiTui ▴ 20
Hello Pierre, Thanks for your reply and insight. with samtools view | grep using the erroneous CIGAR string I get: A00152:841:H7J22D…
Comment: Invalid CIGAR after using bam clipOverlap by Pierre Lindenbaum 162k
please, show us the following output: samtools view "${Ind1}_sorted_dup.bam" | grep -F "A00152:841:H7J22DRX3:2:1112:5267:11397" Furth…
Comment: Failed to download data from EBI with ascp by 孝中 • 0
Hi, have you found the solution to this problem?
Comment: samtools write-index by R.L. • 0
Oh God, thank you so much for helping me in both platforms! I am gonna upgrade my samtools to stay tracked with you and your team! Thank yo…
Answer: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by jared.andrews07 ★ 17k
Go back to your original counts matrix or input data and assign consistent IDs during its generation.
Answer: Facing problem with single cell rna seq annotation using singleR by jared.andrews07 ★ 17k
A few things. >(1)What did i do wrong here? SingleR will annotate each cell with whatever it's most similar to in the reference datas…
Comment: Harmony integration group.by.var parameter by jared.andrews07 ★ 17k
Couldn't tell you, I avoid Seurat like the plague.
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