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733 results • Page
2 of 15
Sort: Rank
Rank
Views
Votes
Replies
362
votes
82
replies
144k
views
35 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
updated 4 weeks ago by
jena
▴ 290 • written 11.2 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 12 months ago by
Ram
43k • written 12 months ago by
Nicola
▴ 10
0
votes
1
reply
431
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
Ram
43k • written 12 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 12 months ago by
Charles-Alexandre Roy
▴ 50 • written 7.4 years ago by
Abdul Rafay Khan
★ 1.2k
4
votes
0
replies
871
views
Tool:
PyComplexHeatmap: a Python package to visualize multimodal genomics data
visualization
Python
ComplexHeatmap
PyComplexHeatmap
16 days ago by
Wubin
▴ 40
0
votes
0
replies
358
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
4.5k
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
802
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
675
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
433
views
Tool:
FungiExpresZ: an intuitive package for fungal gene expression data analysis, visualization and discovery
r
gene-expression
RNA-seq
fungi
updated 13 months ago by
Ram
43k • written 14 months ago by
Chirag Parsania
★ 2.0k
0
votes
0
replies
473
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 14 months ago by
Shuzhi
• 0
1
vote
0
replies
442
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
735
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
9 months ago by
vytarasov
▴ 180
2
votes
0
replies
455
views
Tool:
GeneWarrior is now open source
open
source
15 months ago by
r.follador
▴ 90
0
votes
0
replies
600
views
Tool:
split pooled paired-end fastq using fqkit
fastq
split
barcode
updated 15 months ago by
GenoMax
141k • written 15 months ago by
size_t
▴ 120
1
vote
0
replies
774
views
Tool:
Mabs, a parameter optimizer for Hifiasm and Flye
assembly
7 months ago by
shelkmike
★ 1.2k
1
vote
2
replies
708
views
Tool:
UUIDtoBarcode Renaming of Folders
UUIDtoBarcode
R
updated 16 months ago by
Zhenyu Zhang
★ 1.2k • written 16 months ago by
Kaia
▴ 10
4
votes
0
replies
535
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
444
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
mavy
▴ 10 • written 17 months ago by
Sasha
▴ 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
Wayne
★ 2.0k • written 17 months ago by
moshi
▴ 150
4
votes
2
replies
1.2k
views
Tool:
Introducing Cramino: a *fast* QC tool for long reads
long-read
nanopore
pacbio
updated 21 days ago by
Ram
43k • written 18 months ago by
WouterDeCoster
47k
1
vote
1
reply
525
views
Tool:
trackBrowser: Visualization of sequencing data within a given genome region
RNA
browser
modification
updated 17 months ago by
Alex Reynolds
35k • written 18 months ago by
lsp03yjh
▴ 860
3
votes
1
reply
850
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
715
views
Tool:
Rethinking containers for cloud native pipelines
workflow
container
pipeline
nextflow
18 months ago by
Marcel Ribeiro-Dantas
▴ 470
2
votes
0
replies
828
views
Tool:
Query and annotate variants with gnomAD python
sql
disease
variants
python
gnomad
18 months ago by
Kalin
▴ 50
0
votes
0
replies
343
views
Tool:
Binding free energy
Binding-free-energy
MD-simulation
updated 16 months ago by
Ram
43k • written 18 months ago by
gustmarq4
• 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
Ram
43k • written 7.2 years ago by
Brian Bushnell
20k
1
vote
2
replies
623
views
Tool:
Easy phylogenomics by BuscoPhylo
Phylogenomics
19 months ago by
slimane.khayi
▴ 80
0
votes
0
replies
555
views
Tool:
CZ CELLxGENE - Single-cell visualization and analysis tool
visualization
scRNA-seq
rna-seq
updated 11 months ago by
Ram
43k • written 20 months ago by
mczerwinski
▴ 40
2
votes
1
reply
649
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
477
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
477
views
Tool:
Briefings in Bioinformatics: Hiplot visualization toolkit
data-mining
visualization
updated 21 months ago by
Ram
43k • written 22 months ago by
Jianfeng
▴ 10
2
votes
1
reply
729
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
▴ 740 • written 22 months ago by
PeterC_NCBI
▴ 410
2
votes
5
replies
956
views
Tool:
Latest release of NCBI Magic-BLAST now available
BLAST
NCBI
Magic-BLAST
updated 21 months ago by
GenoMax
141k • written 22 months ago by
PeterC_NCBI
▴ 410
4
votes
0
replies
675
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
880
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
963
views
Tool:
OakVar: genomic variant analysis tool
genomics
variant
updated 16 months ago by
Ram
43k • written 23 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
440
views
Tool:
BIRCH Bioinformatics System v3.86
genomics
sequence
blast
transcriptomics
23 months ago by
brian.fristensky
▴ 460
1
vote
4
replies
810
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
Ram
43k • written 7.7 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 10 months ago by
Ram
43k • written 6.1 years ago by
egeulgen
★ 1.3k
16
votes
3
replies
11k
views
Tool:
Vcflib Documentation
vcf
updated 10 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 10 months ago by
Ram
43k • written 8.0 years ago by
John
13k
76
votes
14
replies
13k
views
10 follow
Tool:
karyoploteR: uncircle your genomes
karyoploteR
Rdataviz
NGS
updated 10 months ago by
Ram
43k • written 6.9 years ago by
bernatgel
★ 3.4k
0
votes
0
replies
415
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
391
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
2.0 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
Calculate Allele balance by sample
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
Answer: Is there a tool that sorts gtf files?
Answer: gvcf joint calling
Answer: Heatmap and rna-seq
Answer: How to use limma to find differentially expressed genes in response to a continu
A: Blast Settings For Short Sequences
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Recent Awards •
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Popular Question
to
rohitsatyam102
▴ 850
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to
candron
▴ 10
Scholar
to
Alex Reynolds
35k
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chaco001
▴ 40
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141k
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BioinfGuru
★ 1.7k
Recent Replies
Comment: different FeatureCounts output for the same data
by
Istvan Albert
100k
just to clarify, it is not that the program algorithm works differently but the meaning of the flags changed; before -p was sufficient to…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★ 1.7k
Thanks Ram. Using merge maxed out my ram on a large list, but your suggestion directed me to purrr::reduce which works great.
Comment: ScRNA data question
by
starswillfade
▴ 10
features <- SelectIntegrationFeatures(object.list = merged_dat) data.anchors <- FindIntegrationAnchors(object.list = merged_dat, …
Comment: gvcf joint calling
by
zihanss
• 0
Thank you for your help! I really appreciate it! And you know, the merged WES gVCF files still have "NA" loci. For such cases, I am quite …
Comment: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
by
Guille
• 0
Thank you for your answer! The MDS plot seems to group most treatment groups close-by, so I'm starting to suspect the effect of treatment …
Answer: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
by
Mensur Dlakic
★ 27k
They say that we remember better things we figured out on our own, rather than things we were taught. You were literally two clicks away fr…
Comment: Heatmap and rna-seq
by
dsull
★ 5.8k
https://maayanlab.cloud/clustergrammer/ It's a web-based tool (can also be a python jupyter widget) that I find useful for exploring a pat…
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
by
Gordon Smyth
★ 7.0k
There is an Agilent array case study in the limma User's Guide, which you might find helpful and somewhat simpler. I don't recommend col…
Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
by
Gordon Smyth
★ 7.0k
The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1. Have you exam…
Answer: How to use limma to find differentially expressed genes in response to a continu
by
Gordon Smyth
★ 7.0k
There's no need for form a contrast because the score variable is already in the model. A continuous variable is its own contrast. Just run…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Thank you Pierre! I'll try this out with my full data set.
Answer: DNA methylation preprocessing
by
cao510927
▴ 30
I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Alex Reynolds
35k
I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
Comment: Highest variable features in single cell data
by
bk11
★ 2.4k
You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
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