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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 5 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 13 months ago by
Ram
43k • written 13 months ago by
Nicola
▴ 10
0
votes
1
reply
435
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
884
views
Tool:
PyComplexHeatmap: a Python package to visualize multimodal genomics data
visualization
Python
ComplexHeatmap
PyComplexHeatmap
25 days ago by
Wubin
▴ 40
0
votes
0
replies
361
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
811
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
681
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
441
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
482
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
447
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
752
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
460
views
Tool:
GeneWarrior is now open source
open
source
16 months ago by
r.follador
▴ 90
0
votes
0
replies
609
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
781
views
Tool:
Mabs, a parameter optimizer for Hifiasm and Flye
assembly
7 months ago by
shelkmike
★ 1.2k
1
vote
2
replies
715
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
542
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
453
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 4 weeks ago by
Ram
43k • written 18 months ago by
WouterDeCoster
47k
1
vote
1
reply
530
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
858
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
728
views
Tool:
Rethinking containers for cloud native pipelines
workflow
container
pipeline
nextflow
18 months ago by
Marcel Ribeiro-Dantas
▴ 470
2
votes
0
replies
836
views
Tool:
Query and annotate variants with gnomAD python
sql
disease
variants
python
gnomad
18 months ago by
Kalin
▴ 50
0
votes
0
replies
348
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
14k
views
10 follow
Tool:
BBSketch - A Tool for Rapid Sequence Comparison
minhash
sketch
bbmap
blast
updated 11 months ago by
Ram
43k • written 7.3 years ago by
Brian Bushnell
20k
1
vote
2
replies
633
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
Ram
43k • written 20 months ago by
mczerwinski
▴ 40
2
votes
1
reply
661
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
483
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
481
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
735
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
▴ 760 • written 22 months ago by
PeterC_NCBI
▴ 410
2
votes
5
replies
974
views
Tool:
Latest release of NCBI Magic-BLAST now available
BLAST
NCBI
Magic-BLAST
updated 21 months ago by
GenoMax
142k • written 22 months ago by
PeterC_NCBI
▴ 410
4
votes
0
replies
679
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
967
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
445
views
Tool:
BIRCH Bioinformatics System v3.86
genomics
sequence
blast
transcriptomics
23 months ago by
brian.fristensky
▴ 460
1
vote
4
replies
822
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 6.2 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 8.1 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
420
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
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
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
DEXSeq multiple time points
How to find the most frequent alternative-splicing event from DEXSEQ data?
Comment: Design matrix Differential expression analysis
UMI-Tools 0.5, now with tools for cell barcoded scRNA-seq
Comment: install.packages("imudata")
Answer: Can I merge Hi-C fastq files from different lanes?
Answer: Interpretation of output from MiXCR TCR sequencing
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Comment: Design matrix Differential expression analysis
by
SHN
▴ 40
Got it, thank you for your response. SN
Comment: How to interpret DEXseq results in therms of significance
by
Sara
▴ 30
Hi, I used write.table(as.data.frame(DEXSeqResults(MyObj)), "Results.tsv", quote=FALSE, sep="\t", dec=".") to save the result but I recei…
Comment: Tissue-specific DEG analysis with DEseq2
by
M.
▴ 30
Can I ask what do you exactly mean by same experiment? If you are talking about the same donor and the same procedure, unfortunately, not a…
Comment: install package: package ‘gmwm’ is not available for this version of R
by
Ram
43k
Find someone with computer skills near you and consult them. From your posts on the forum, it's clear that you need help at a level that we…
Comment: Gene Specific coverage from WGS data
by
GenoMax
142k
This is not going to work no matter what program you use since the chromosome identifiers in your GTF (`MN908947.3 `) do not match your BA…
Comment: install.packages("imudata") - package ‘imudata’ is not available for this versio
by
Ram
43k
Read the answers in the post, understand them and try to implement them.
Comment: High Malat-1 expression in single cell data
by
t.montserrat.ayuso
▴ 10
Just using the normalized expression of Malat1 works.
Comment: Can I merge Hi-C fastq files from different lanes?
by
Winter
• 0
Awesome, thank you for the concise and straight-forward answer!
Comment: error in R code
by
ATpoint
82k
Look, before you keep posting these sorts of questions and might gross of users, please read and follow https://www.biostars.org/p/357878/ …
Comment: Gene Specific coverage from WGS data
by
1769mkc
★ 1.2k
"Also if is there any other quick way to find gene specific coverage" can you give some example so that its bit more clear what do you mean…
Answer: Tissue-specific DEG analysis with DEseq2
by
ATpoint
82k
I assume that all data are from the same experiment, without batch effects and can thus be quantitiatively compared: Many ways to do thi…
Comment: install.packages("imudata") - package ‘imudata’ is not available for this versio
by
snajafy
• 0
I am facing the same problem and I don't know how to solve the problem,....
Comment: install.packages("imudata")
by
zx8754
11k
[How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning?](https://stackoverflow.com/q/25721884/680068)
Answer: install.packages("imudata")
by
ATpoint
82k
Welcome to this community. Please learn the most important lesson right away which is reading answers and learning from it. Users gave you …
Comment: install.packages("imudata")
by
marco.barr
▴ 90
You can install from github directly. Many R packages are not present in the CRAN repository or in Bioconductor( from Biocmanager). Also re…
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