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734 results • Page 2 of 15
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460
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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
440
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
903
views
Tool: PyComplexHeatmap: a Python package to visualize multimodal genomics data
visualization Python ComplexHeatmap PyComplexHeatmap
4 weeks ago by Wubin ▴ 40
0
votes
0
replies
363
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
819
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
14 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
449
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
758
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
1 day 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
784
views
Tool: Mabs, a parameter optimizer for Hifiasm and Flye
assembly
7 months ago by shelkmike ★ 1.2k
1
vote
2
replies
716
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
550
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
457
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 18 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 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 5 weeks ago by 43k • written 18 months ago by 47k
1
vote
1
reply
533
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
864
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
734
views
Tool: Rethinking containers for cloud native pipelines
workflow container pipeline nextflow
18 months ago by Marcel Ribeiro-Dantas ▴ 470
2
votes
0
replies
842
views
Tool: Query and annotate variants with gnomAD python
sql disease variants python gnomad
19 months ago by Kalin ▴ 50
0
votes
0
replies
351
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
639
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
670
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
483
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
982
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
684
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
973
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
827
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 7.8 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 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
423
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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Answer: Server or aws cloud- which one is better for gatk pipeline
Comment: How to remove multiple batch effects from RNA-seq data before limma differential
Comment: automatic clustering annotation using python
automatic clustering annotation using python
Answer: How to compute TPM normalized values for TCGA miRNA data?
C: Convert .Txt File To Bed File
A: Get nonoverlapping regions of two bed files
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Answer: CNVKIT - unable to produce scatter and diagram pdfs by Anitha • 0
While running with this batch option batch --method wgs option. I have used this command " cnvkit.py batch tumor.bam -n normal.bam -m wgs -…
Answer: Generating .bed file and .map file for polyploid vcf file through plink by chrchang523 10k
Why do you think ADMIXTURE supports polyploid input? (Note that this is an answer, not a comment.)
Comment: How to convert normalized BigWig file to count matrix? by feather-W • 0
Hi ATpoint, Thanks for your reply!
Comment: How to convert normalized BigWig file to count matrix? by feather-W • 0
Hi Pierre, Thanks for your reply! I want to get a feature count matrix from coverage data stored in BigWig files. And this BigWig file ha…
Comment: Extracting mutation status from MAF files - TCGA by Zhenyu Zhang ★ 1.2k
you can assume all genes without mutation is WT (easy) while controlling for (difficult) - coverage - capture region - germline - the …
Comment: Obtaining Infinium Methylation450K manifest for hg38 by Zhenyu Zhang ★ 1.2k
Since you are getting data from the GDC, analysis-related reference/annotations can be found in the GDC reference page here https://gdc.can…
Comment: Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in py by fracarb8 ★ 1.6k
I saw that, but considering that your analysis is in seurat and that both liana and liana+ are from the same developers, it might be quicke…
Answer: Nomalization - TCGA, RNA-seq and Microarray by Zhenyu Zhang ★ 1.2k
You can rank normalize them, but to tell the truth, I won't trust any conclusion you can draw from such combined data. The recommended …
Comment: How to remove multiple batch effects from RNA-seq data before limma differential by ATpoint 82k
Include confounders into the limma design. No need for upfront removal. Note that libsize is taken care of by normalizing usually. Are you …
Comment: Longest transcript variant per gene by sansan_96 ▴ 90
Thank you very much, success in your projects.
Comment: In IGV is this a heterogeneous mutation or false call? by Tuck898 • 0
Thanks for the input :)
Comment: install package: package ‘gmwm’ is not available for this version of R by Pine ▴ 20
This seems to indicate that the package itself (or packages it depends on) are not compatible with the R version you are using. Next step c…
Answer: Tissue-specific DEG analysis with DEseq2 by arctic ▴ 40
Not my area of expertise but GTEx portal seems to offer visual comparison of expression across tissues, maybe checking their pipeline could…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File by Pierre Lindenbaum 161k
> I think I am mostly struggling with what would need to be coded to my dataset here and how to run this loop on my set in general. i do…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File by ajbarrett98 • 0
Pierre, I am a novice at all of this in general and I have never used Java-based programming before. I may not be able to properly wrangl…
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