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735 results • Page
2 of 15
Sort: Rank
Rank
Views
Votes
Replies
1
vote
2
replies
875
views
Tool:
Tinybio Slackbot - a large language model slackbot for bioinformatics
qa
12 months ago by
Sasha
▴ 840
0
votes
0
replies
463
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
jena
▴ 290 • written 11.3 years ago by
ole.tange
★ 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
Ram
43k • written 13 months ago by
Nicola
▴ 10
0
votes
1
reply
442
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
Ram
43k • written 13 months ago by
Xuewen
• 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
Charles-Alexandre Roy
▴ 50 • written 7.4 years ago by
Abdul Rafay Khan
★ 1.2k
4
votes
0
replies
911
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
Ram
43k • written 13 months ago by
vytarasov
▴ 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
Ram
43k • written 8.2 years ago by
Csaba Kerepesi
▴ 350
2
votes
2
replies
820
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
687
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
447
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
Ram
43k • written 14 months ago by
Chirag Parsania
★ 2.0k
0
votes
0
replies
487
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
Ram
43k • written 15 months ago by
Shuzhi
• 0
1
vote
0
replies
450
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
761
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
4 days 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
614
views
Tool:
split pooled paired-end fastq using fqkit
fastq
split
barcode
updated 16 months ago by
GenoMax
142k • written 16 months ago by
size_t
▴ 120
1
vote
0
replies
785
views
Tool:
Mabs, a parameter optimizer for Hifiasm and Flye
assembly
8 months ago by
shelkmike
★ 1.2k
1
vote
2
replies
719
views
Tool:
UUIDtoBarcode Renaming of Folders
UUIDtoBarcode
R
updated 17 months ago by
Zhenyu Zhang
★ 1.2k • written 17 months ago by
Kaia
▴ 10
4
votes
0
replies
553
views
Tool:
Visual analysis of VCF files
vcf
visual-analysis
updated 17 months ago by
Ram
43k • written 17 months ago by
cocchi.e89
▴ 270
1
vote
0
replies
457
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
mavy
▴ 10 • written 18 months ago by
Sasha
▴ 840
4
votes
2
replies
2.7k
views
Tool:
pyMSAviz - MSA visualization python package for sequence analysis
visualization
MSA
Python
updated 18 months ago by
Wayne
★ 2.0k • written 18 months ago by
moshi
▴ 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
Ram
43k • written 18 months ago by
WouterDeCoster
47k
1
vote
1
reply
534
views
Tool:
trackBrowser: Visualization of sequencing data within a given genome region
RNA
browser
modification
updated 18 months ago by
Alex Reynolds
35k • written 18 months ago by
lsp03yjh
▴ 860
3
votes
1
reply
865
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
739
views
Tool:
Rethinking containers for cloud native pipelines
workflow
container
pipeline
nextflow
19 months ago by
Marcel Ribeiro-Dantas
▴ 470
2
votes
0
replies
843
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
Ram
43k • written 19 months ago by
gustmarq4
• 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
Ram
43k • written 7.3 years ago by
Brian Bushnell
20k
1
vote
2
replies
639
views
Tool:
Easy phylogenomics by BuscoPhylo
Phylogenomics
20 months ago by
slimane.khayi
▴ 80
0
votes
0
replies
560
views
Tool:
CZ CELLxGENE - Single-cell visualization and analysis tool
visualization
scRNA-seq
rna-seq
updated 12 months ago by
Ram
43k • written 21 months ago by
mczerwinski
▴ 40
2
votes
1
reply
672
views
Tool:
Best-practice bulk RNA-seq workflow with citations
rnaseq
sequencing
bulkrnaseq
rna
updated 21 months ago by
Kenny
▴ 30 • written 21 months ago by
Kenny
▴ 20
2
votes
0
replies
487
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
Ram
43k • written 22 months ago by
Jianfeng
▴ 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
Jesse
▴ 770 • written 22 months ago by
PeterC_NCBI
▴ 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
GenoMax
142k • written 22 months ago by
PeterC_NCBI
▴ 410
4
votes
0
replies
689
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
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
976
views
Tool:
OakVar: genomic variant analysis tool
genomics
variant
updated 17 months ago by
Ram
43k • written 24 months ago by
Ryangguk Kim
▴ 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
Lior Pachter
▴ 700 • written 23 months ago by
Laura Luebbert
▴ 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
830
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 11 months ago by
Ram
43k • written 7.8 years ago by
thomaskuilman
▴ 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
Ram
43k • written 6.2 years ago by
egeulgen
★ 1.3k
16
votes
3
replies
11k
views
Tool:
Vcflib Documentation
vcf
updated 11 months ago by
Ram
43k • written 11.1 years ago by
Erik Garrison
★ 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
Ram
43k • written 8.1 years ago by
John
13k
76
votes
14
replies
13k
views
10 follow
Tool:
karyoploteR: uncircle your genomes
karyoploteR
Rdataviz
NGS
updated 11 months ago by
Ram
43k • written 6.9 years ago by
bernatgel
★ 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
735 results • Page
2 of 15
Recent Votes
Answer: Doubt about the process of annotation, detection, identification and classificat
Answer: Filtering VCF files based on VAF giving incorrect results
Problems with breakdancer (sv caller) output.
Problems with breakdancer (sv caller) output.
Comment: Add stats to boxplot in R
Answer: Genotyping sites with N in reference genome
A: how to combine RNA seq data from 4 lanes
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Recent Awards •
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Popular Question
to
Jean-Karim Heriche
27k
Popular Question
to
Chironex
▴ 40
Scholar
to
rpolicastro
13k
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to
Amr
▴ 160
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asalimih
▴ 60
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nd48
▴ 20
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Trivas
★ 1.8k
Recent Replies
Comment: Doubt about the process of annotation, detection, identification and classificat
by
MarcosCosta
• 0
Thank you very much, you've helped me a lot
Comment: Filtering VCF files based on VAF giving incorrect results
by
Arton
• 0
Thank you. I can't try a completely new tool but I will keep your command for future use. Do you think my commands were correct? For exampl…
Comment: Add stats to boxplot in R
by
Ghada
• 0
Thanks. Thats work
Comment: Genotyping sites with N in reference genome
by
Zhenyu Zhang
★ 1.2k
Whether N -> A/T/G/C represents a variant is heavily dependent on the tool itself, and I know most tools don't. Since you don't see it in y…
Comment: calculating genomic coverage/ base overlap in R
by
marco.barr
▴ 110
The code seems correct at first glance... How did you generate the data in the Excel file? Have you checked the exon annotations? You could…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Did you remeber to unzip/untar the `nt` preformatted files that you downloaded?
Comment: Genotyping sites with N in reference genome
by
shpak.max
▴ 50
Just to clarify, I have set additional sites in the reference genome to 'N', which means (based on your statement) that these will not be g…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Pierre Lindenbaum
161k
see https://www.biostars.org/p/9496674/ <!-- when i runed blastn(version 2.15) and nt database(latest version). I used aspera to download…
Answer: Genotyping sites with N in reference genome
by
Pierre Lindenbaum
161k
> Does UnifiedGenotyper skip/ignore sites where the reference genotype is N yes. The variant is in YOUR data, not in the reference where '…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
yura.grabovska
▴ 70
Do you have samples that should in theory have a good degree over overlap in terms of cell types across the two sequencing types? I would …
Comment: Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
by
asalimih
▴ 60
I found out that vep is only checking the GT field therefore assigning HOM to the Zygosity. Therefore the problem should be from deepvarian…
Comment: Add stats to boxplot in R
by
Lélé
▴ 10
To remove "Kruskall Wallis" you can try adding the argument label="p" or label = "p.signif" which displays the p-value or *** like this: …
Answer: Sequencing Depth (Read Depth) Calculations
by
GenoMax
142k
You could also use `pandepth` ([**LINK**][1]) or `mosdepth` ([**LINK**][2]) as well. These will allow you to be flexible about windowed cov…
Comment: Sequencing Depth (Read Depth) Calculations
by
Pierre Lindenbaum
161k
it looks looks ok to me. <!-- This cmd works and gives me 40.5235, I was wondering whether this cmd is right or wrong, and does anyone hav…
Comment: Add stats to boxplot in R
by
Ghada
• 0
Great. thats work. Do you know how can I remove the kruskall-Wallis name from the plot? Also I would like to draw a line under the kruskall…
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