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736 results • Page 2 of 15
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Tool: Single-cell RNA-seq data analysis tool Cellenics®
single-cell RNA-seq scRNA-seq
updated 12 months ago by 43k • written 12 months ago by • 0
0
votes
1
reply
994
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 43k • written 12 months ago by • 0
1
vote
2
replies
878
views
Tool: Tinybio Slackbot - a large language model slackbot for bioinformatics
qa
12 months ago by Sasha ▴ 850
0
votes
0
replies
466
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 7 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 43k • written 13 months ago by ▴ 10
0
votes
1
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444
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 7.5 years ago by ★ 1.2k
4
votes
0
replies
921
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
366
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
821
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
690
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
449
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 15 months ago by ★ 2.0k
0
votes
0
replies
490
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 43k • written 15 months ago by • 0
1
vote
0
replies
453
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
766
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
9.8k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
6 days ago by vytarasov ▴ 180
2
votes
0
replies
463
views
Tool: GeneWarrior is now open source
open source
16 months ago by r.follador ▴ 90
0
votes
0
replies
615
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
787
views
Tool: Mabs, a parameter optimizer for Hifiasm and Flye
assembly
8 months ago by shelkmike ★ 1.2k
1
vote
2
replies
722
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
556
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
460
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
1.0k
views
Tool: Tool: Quick Command To Change BED file Naming Convention
bed awk
updated 6 months ago by ▴ 10 • written 18 months ago by ▴ 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 43k • written 18 months ago by 47k
1
vote
1
reply
537
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
870
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
741
views
Tool: Rethinking containers for cloud native pipelines
workflow container pipeline nextflow
19 months ago by Marcel Ribeiro-Dantas ▴ 470
2
votes
0
replies
845
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 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 12 months ago by 43k • written 7.3 years ago by 20k
1
vote
2
replies
641
views
Tool: Easy phylogenomics by BuscoPhylo
Phylogenomics
20 months ago by slimane.khayi ▴ 80
0
votes
0
replies
563
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
2
votes
1
reply
676
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
488
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
484
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
740
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
984
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
695
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
892
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
978
views
Tool: OakVar: genomic variant analysis tool
genomics variant
updated 17 months ago by 43k • 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 23 months ago by ▴ 700 • written 24 months ago by ▴ 450
0
votes
0
replies
450
views
Tool: BIRCH Bioinformatics System v3.86
genomics sequence blast transcriptomics
23 months ago by brian.fristensky ▴ 460
1
vote
4
replies
834
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 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
736 results • Page 2 of 15
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Answer: RNAseq coverage vs depth for transcript isoform expression?
Answer: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
C: How can I perform Differential expression analysis with just one control and one
C: How can I perform Differential expression analysis with just one control and one
C: How can I perform Differential expression analysis with just one control and one
How can I perform Differential expression analysis with just one control and one cancer sample?
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Recent Replies
Comment: Help with Biopython for Beginner by Joe 21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression? by Gordon Smyth ★ 7.2k
See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Our resul…
Comment: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF) by aidangcruickshank ▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data? by Ngrin • 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot by LauferVA 4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot by bk11 ★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool by ntsopoul ▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool by GenoMax 142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by bk11 ★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
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