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733 results • Page 2 of 15
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362
votes
82
replies
144k
views
35 follow
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel next-gen ngs
updated 5 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 12 months ago by 43k • written 12 months ago by ▴ 10
0
votes
1
reply
434
views
Tool: TRcaller : a novel Tool for SSR /STR/TR genotyping from NGS data for short and long reads
SSR NGS genotype STR
updated 12 months ago by 43k • written 12 months ago by • 0
46
votes
9
replies
43k
views
7 follow
Tool: Tools to merge overlapping paired-end reads
ngs Assembly fastq
updated 12 months ago by ▴ 50 • written 7.4 years ago by ★ 1.2k
4
votes
0
replies
880
views
Tool: PyComplexHeatmap: a Python package to visualize multimodal genomics data
visualization Python ComplexHeatmap PyComplexHeatmap
22 days ago by Wubin ▴ 40
0
votes
0
replies
360
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
807
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
680
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
438
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
479
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
445
views
Tool: HaploCart: Human mtDNA Haplogroup Classification Using a Pangenomic Reference Graph
graph human pangenome haplogroup mitochondrion
14 months ago by Gabriel R. ★ 2.9k
5
votes
0
replies
749
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
458
views
Tool: GeneWarrior is now open source
open source
16 months ago by r.follador ▴ 90
0
votes
0
replies
606
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
779
views
Tool: Mabs, a parameter optimizer for Hifiasm and Flye
assembly
7 months ago by shelkmike ★ 1.2k
1
vote
2
replies
712
views
Tool: UUIDtoBarcode Renaming of Folders
UUIDtoBarcode R
updated 16 months ago by ★ 1.2k • written 16 months ago by ▴ 10
4
votes
0
replies
538
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
448
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 5 months ago by ▴ 10 • written 17 months ago by ▴ 840
4
votes
2
replies
2.6k
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
1.2k
views
Tool: Introducing Cramino: a *fast* QC tool for long reads
long-read nanopore pacbio
updated 28 days ago by 43k • written 18 months ago by 47k
1
vote
1
reply
527
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
856
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
725
views
Tool: Rethinking containers for cloud native pipelines
workflow container pipeline nextflow
18 months ago by Marcel Ribeiro-Dantas ▴ 470
2
votes
0
replies
830
views
Tool: Query and annotate variants with gnomAD python
sql disease variants python gnomad
18 months ago by Kalin ▴ 50
0
votes
0
replies
346
views
Tool: Binding free energy
Binding-free-energy MD-simulation
updated 16 months ago by 43k • written 18 months ago by • 0
26
votes
22
replies
13k
views
10 follow
Tool: BBSketch - A Tool for Rapid Sequence Comparison
minhash sketch bbmap blast
updated 11 months ago by 43k • written 7.2 years ago by 20k
1
vote
2
replies
631
views
Tool: Easy phylogenomics by BuscoPhylo
Phylogenomics
20 months ago by slimane.khayi ▴ 80
0
votes
0
replies
558
views
Tool: CZ CELLxGENE - Single-cell visualization and analysis tool
visualization scRNA-seq rna-seq
updated 11 months ago by 43k • written 20 months ago by ▴ 40
2
votes
1
reply
657
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
480
views
Tool: NCBI's BLAST ClusteredNR database results have in-cluster analysis
BLAST NCBI ClustereedNR
21 months ago by PeterC_NCBI ▴ 410
1
vote
0
replies
478
views
Tool: Briefings in Bioinformatics: Hiplot visualization toolkit
data-mining visualization
updated 21 months ago by 43k • written 22 months ago by ▴ 10
2
votes
1
reply
734
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 ▴ 740 • written 22 months ago by ▴ 410
2
votes
5
replies
970
views
Tool: Latest release of NCBI Magic-BLAST now available
BLAST NCBI Magic-BLAST
updated 21 months ago by 142k • written 22 months ago by ▴ 410
4
votes
0
replies
678
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
884
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
966
views
Tool: OakVar: genomic variant analysis tool
genomics variant
updated 16 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
443
views
Tool: BIRCH Bioinformatics System v3.86
genomics sequence blast transcriptomics
23 months ago by brian.fristensky ▴ 460
1
vote
4
replies
817
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 6.1 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
419
views
Tool: Announcing the Papilloma Virus Episteme (PaVE) 2.0 Release
genomics HPV 3D
2.0 years ago by karlynn.noble ▴ 60
0
votes
0
replies
395
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
9
votes
7
replies
1.7k
views
Tool: miniDBG - a Jupyter notebook for teaching De Bruijn Graph assembly
python deBruijnGraph de_bruijn_graph assembly teaching
2.0 years ago by Michael 54k
733 results • Page 2 of 15
Recent Votes
how to combine multiple RNAseq count files into a single dataframe in R and unix
Comment: Greatly speed up conda by using mamba
Greatly speed up conda by using mamba
Comment: Converting CRAM to FastQ
Parametric or non-parametric tests for qPCR significance testing between treatments?
Answer: Converting CRAM to FastQ
Answer: Does comparing two different groups to a common third group introduce bias in th
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Answer: Differential Expression Analysis using DESeq2 in R by Erina • 0
![Here is the code I am using for the analysis][1] [1]: /media/images/8a511904-6ae8-47f5-b647-ee15b02b
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read by swbarnes2 14k
In paired end sequencing, every read has a mate, and the flags all together tell you not only what is up with the read you are looking at, …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by Mbofire • 0
I need assistance don't know what to do next after signing up
Comment: Easy way to find out which allele is minor allele from bed file? by curious ▴ 750
According to the link: "When *generating* such filesets, PLINK 1.x defaults to swapping the alleles whenever A1's frequency is above (not …
Comment: TaxID mapping file by GenoMax 142k
nodesDB file should have been installed if you had used "Install" script for `blobtools` according to : https://blobtools.readme.io/docs/ta…
Comment: Parametric or non-parametric tests for qPCR significance testing between treatme by e.r.zakiev ▴ 210
obviously if the values are really sampled from a (quasi) normally-distributed values, then n doesn't matter, he could use t-test even with…
Comment: Converting CRAM to FastQ by Maverick ▴ 10
Understood Thank you!
Comment: Converting CRAM to FastQ by GenoMax 142k
You can use any reference that you like at this point. Since you are planning to use GATK, you can get their version from the resource bund…
Comment: Converting CRAM to FastQ by Maverick ▴ 10
![enter image description here][1]I was able to get my fastq files. I can see that my reference files are cached in a hts-ref directory but…
Comment: Differential Expression Analysis using DESeq2 in R by swbarnes2 14k
Okay, that shows us the problem, but not what we need to solve it. But, for instance, are you sure that period after the sample name shou…
Comment: Easy way to find out which allele is minor allele from bed file? by bk11 ★ 2.4k
In the case of MAF = 0.5, I think A1 is still the minor allele. You can check the discussion in this [link][1]. [1]: https://groups.goo…
Comment: Easy way to find out which allele is minor allele from bed file? by curious ▴ 750
Yes, but I think the problem is what to do when MAF = 0.5
Answer: Easy way to find out which allele is minor allele from bed file? by bk11 ★ 2.4k
In Plink, A1 is usually a minor allele and A2 a major allele. .frq (basic allele frequency report) Produced by --freq. …
Comment: Raw counts using stringtie by GenoMax 142k
> Error parsing strand from GFF line Looking at this error and the listing of files in your directory it looks like you need to `gunzip` t…
Comment: High Malat-1 expression in single cell data by dsull ★ 6.0k
I briefly looked at those genes on a genome browser -- there are a lot of repeat elements in those genes, meaning a lot of counts assigned …
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