Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this year
all time
today
this week
this month
this year
517 results • Page
2 of 11
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 7 weeks ago by
jena
▴ 290 • written 11.3 years ago by
ole.tange
★ 4.4k
4
votes
0
replies
915
views
Tool:
PyComplexHeatmap: a Python package to visualize multimodal genomics data
visualization
Python
ComplexHeatmap
PyComplexHeatmap
5 weeks ago by
Wubin
▴ 40
9
votes
23
replies
9.8k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
5 days ago by
vytarasov
▴ 180
1
vote
0
replies
785
views
Tool:
Mabs, a parameter optimizer for Hifiasm and Flye
assembly
8 months ago by
shelkmike
★ 1.2k
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
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
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
0
votes
0
replies
561
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
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 11.2 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
2
votes
0
replies
594
views
Tool:
Introducing ElasticBLAST – Run bigger BLAST searches faster on the Cloud
ElasticBLAST
BLAST
NCBI
updated 11 months ago by
Ram
43k • written 2.1 years ago by
PeterC_NCBI
▴ 410
231
votes
38
replies
146k
views
29 follow
Tool:
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl
genome-coordinates
liftover
updated 11 months ago by
Ram
43k • written 11.2 years ago by
Malachi Griffith
20k
5
votes
2
replies
2.4k
views
Tool:
eLabFTW: a free and open source electronic lab notebook
elabftw
free-open-source-software
php
updated 11 months ago by
Ram
43k • written 4.7 years ago by
Nico
▴ 190
1
vote
1
reply
3.7k
views
Tool:
mirDIP 4.1 - integrative database of human microRNA target predictions
interactome
miRNA
targets
microRNA
updated 11 months ago by
Ram
43k • written 6.0 years ago by
tomastokar
▴ 50
2
votes
6
replies
3.4k
views
Tool:
microbiomeMarker: microbiome biomarker analysis in R
stamp
microbiome
lefse
updated 11 months ago by
Ram
43k • written 3.9 years ago by
yiluheihei
▴ 30
5
votes
8
replies
7.0k
views
6 follow
Tool:
Converting MUMmer snps file to a real VCF file
VCF
mummer
SNP
updated 11 months ago by
Ram
43k • written 4.7 years ago by
Matteo Schiavinato
★ 3.6k
15
votes
11
replies
8.3k
views
Tool:
Arriba: Fast and accurate gene fusion detection from RNA-Seq data
variant-calling
RNA-Seq
cancer
gene-fusion
updated 11 months ago by
Ram
43k • written 6.3 years ago by
uhrigs
▴ 150
28
votes
17
replies
5.1k
views
7 follow
Tool:
PCAtools: everything Principal Components Analysis
eigenvector
pca
bioconductor
R
updated 11 months ago by
Ram
43k • written 5.3 years ago by
Kevin Blighe
88k
10
votes
5
replies
2.5k
views
Tool:
Genozip: A new compression tool for FASTQ, BAM, VCF and more
bam
vcf
fastq
compression
10 months ago by
Divon
▴ 230
4
votes
13
replies
2.8k
views
Tool:
SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
pathway-analysis
visualization
Pathview
SBGN
updated 11 months ago by
Ram
43k • written 3.2 years ago by
bigmawen
▴ 430
3
votes
5
replies
2.8k
views
Tool:
Extend 3' UTR of a GTF file
annotation
python
RNA-Seq
GTF
updated 11 months ago by
Ram
43k • written 3.6 years ago by
Shred
★ 1.4k
50
votes
16
replies
14k
views
12 follow
Tool:
Omictools: A didactic directory for omic data analysis (NGS, microarray, PCR, MS, NMR)
pcr
software
ngs
updated 11 months ago by
Ram
43k • written 10.7 years ago by
arnaud.desfeux
▴ 450
21
votes
14
replies
9.5k
views
Tool:
trackplot: Fast and minimal dependency standalone R script to generate IGV style locus tracks from bigWig files
visualization
igv
ChIP-Seq
R
bigwigs
updated 11 months ago by
Ram
43k • written 3.5 years ago by
poisonAlien
★ 3.2k
9
votes
7
replies
3.0k
views
Tool:
DiffBind 3.0: Extensive updates in Bioconductor 3.12
DiffBind
ChIP-Seq
diffbind
ATAC-seq
chipseq
updated 11 months ago by
Ram
43k • written 3.5 years ago by
Rory Stark
★ 2.0k
0
votes
1
reply
1.1k
views
Tool:
Compi: Application Framework for Portable Computational Pipelines
pipeline
workflow-management-system
docker
updated 11 months ago by
Ram
43k • written 4.6 years ago by
Hugo
▴ 380
4
votes
7
replies
4.6k
views
6 follow
Tool:
MAGERI: a software tool for calling rare variants and detecting circulating tumor DNA from UMI-tagged high-throughput sequencing data
rare-variant
resequencing
umi
ctDNA
updated 3 months ago by
blid11
• 0 • written 7.0 years ago by
mikhail.shugay
3.5k
1
vote
0
replies
600
views
Tool:
Super easy to use free paper retrieval artifact: PyPubMed
python
pubmed
software
updated 11 months ago by
Ram
43k • written 3.0 years ago by
Novogene
▴ 420
0
votes
0
replies
702
views
Tool:
IPC 2.0: prediction of isoelectric point and pKa dissociation constants
deep-learning
isoelectric-point
2D-PAGE
pKa
updated 11 months ago by
Ram
43k • written 3.0 years ago by
Lukasz Kozlowski
• 0
8
votes
6
replies
5.9k
views
Tool:
chromoMap- R package for Interactive visualization and Annotation of chromosomes or regions of any living organism.
annotation
R
genome
visualization
updated 11 months ago by
Ram
43k • written 5.1 years ago by
lakshayanand15
▴ 80
13
votes
14
replies
6.2k
views
9 follow
Tool:
open-cravat: variant annotation tool
open-cravat
updated 11 months ago by
Ram
43k • written 5.4 years ago by
slcrick
▴ 260
2
votes
1
reply
779
views
Tool:
Bioinformatics Programming Package
Package
updated 11 months ago by
Ram
43k • written 3.1 years ago by
Asad Bilal
▴ 10
68
votes
25
replies
16k
views
12 follow
Tool:
sra-explorer : find SRA and FastQ download URLs in a couple of clicks
fastq
SRA
updated 6 months ago by
GenoMax
142k • written 5.2 years ago by
Phil Ewels
★ 1.4k
2
votes
0
replies
861
views
Tool:
New location tracking tool for SARS-CoV-2 variant surveillance
sars-cov-2
variant
covid-19
updated 11 months ago by
Ram
43k • written 3.2 years ago by
ehaag
▴ 20
12
votes
5
replies
6.2k
views
Tool:
AGAT - Another Gff/Gtf Analysis Toolkit
gff
gtf
updated 10 months ago by
Ram
43k • written 4.4 years ago by
Juke34
8.6k
18
votes
39
replies
4.3k
views
Tool:
CBioInfCpp.h as a C++ lib containing some functions for bioinformatics
cpp
updated 12 months ago by
Ram
43k • written 5.1 years ago by
chernouhov sergey
▴ 50
3
votes
1
reply
1.3k
views
Tool:
Introducing Gallia: a Scala library for data manipulation
scala
etl
json
vcf
spark
updated 11 months ago by
Ram
43k • written 3.3 years ago by
cros.anthony
▴ 30
0
votes
0
replies
1.4k
views
Tool:
I made QMplot: a python library and tools of generating high-quality manhattan and Q-Q plots for GWAS data
visualization
Manhattan-Plot
GWAS
genome
Python
updated 11 months ago by
Ram
43k • written 3.2 years ago by
huangshujia9
• 0
15
votes
2
replies
3.1k
views
Tool:
EnhancedVolcano becomes a pseudo-EnhancedMA
enhancedMA
enhancedvolcano
updated 11 months ago by
Ram
43k • written 3.7 years ago by
Kevin Blighe
88k
4
votes
1
reply
1.3k
views
Tool:
rBCS & pyBCS: open-source packages to support interactive visualizations of single-cell data
rna-seq
single-cell
scrna-seq
updated 11 months ago by
Ram
43k • written 3.2 years ago by
Jennifer Pham
▴ 450
0
votes
0
replies
672
views
Tool:
MultiLink Analysis: Brain Network Comparison via Sparse Connectivity Analysis
networks
neuroscience
connectome
brain
updated 11 months ago by
Ram
43k • written 3.3 years ago by
alex.crimi
• 0
1
vote
0
replies
681
views
Tool:
BiOkeanos - the largest(*) biomedical database catalogue and discovery tool
database
catalogue
data
updated 11 months ago by
Ram
43k • written 3.3 years ago by
ellimilial
▴ 20
0
votes
0
replies
844
views
Tool:
Analyze & Visualize Nephele Microbiome Results Using MicrobiomeDB
microbiome
sequence
updated 11 months ago by
Ram
43k • written 3.3 years ago by
karlynn.noble
▴ 60
22
votes
20
replies
4.9k
views
Tool:
elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
sam
bam
bqsr
updated 11 months ago by
Ram
43k • written 5.6 years ago by
Charlotte.Herzeel
▴ 150
7
votes
10
replies
1.5k
views
Tool:
SamReadViewer - A small utility to visualise read alignment directly from sam format without reference.
samreadviewer
updated 11 months ago by
Ram
43k • written 3.6 years ago by
Juke34
8.6k
0
votes
0
replies
632
views
Tool:
Cytoscape Network analysis
software-error
cytoscape
updated 11 months ago by
Ram
43k • written 3.3 years ago by
subhasisdehury
• 0
0
votes
6
replies
1.5k
views
Tool:
Script: Downloading fastq files from ENA database
next-gen-sequencing
RNA-Seq
updated 11 months ago by
Ram
43k • written 3.3 years ago by
jayeshkumarsundaram
• 0
11
votes
2
replies
7.1k
views
Tool:
fastp (the ultra-fast all-in-one FASTQ preprocessing tool) v0.18.0 released, 2X faster, with many new features.
fastp
QC
updated 11 months ago by
Ram
43k • written 5.9 years ago by
chen
★ 2.5k
517 results • Page
2 of 11
Recent Votes
Comment: switch off warning in blast command line
Forward And Reverse Strand Conventions
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Answer: Details on salmon index
ATAC-seq sample normalization
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
Recent Locations •
All
San Francisco,
3 minutes ago
India,
6 minutes ago
Germany,
8 minutes ago
Taiwan,
9 minutes ago
Bologna,
9 minutes ago
India,
10 minutes ago
India,
10 minutes ago
Recent Awards •
All
Teacher
to
Rob
6.6k
Popular Question
to
Nyksubuz
▴ 10
Popular Question
to
Govardhan Anande
▴ 150
Popular Question
to
Lhl
▴ 760
Popular Question
to
Takuma
▴ 20
Popular Question
to
BATMAN
• 0
Teacher
to
dario.garvan
▴ 520
Recent Replies
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Nyksubuz
▴ 10
The dataset you want (taestivum_eg_gene) exists within the "plants_mart" schema, not the default schema. Your current code assumes the defa…
Comment: Add line under stat test
by
Nyksubuz
▴ 10
You could use [this][1] [1]: https://ggplot2.tidyverse.org/reference/geom_segment.html
Comment: API kegg - IndexError: list index out of range
by
Nyksubuz
▴ 10
It might be because the gene symbol is not found in the KEGG database. Add some extra error handling before parsing the results or do a man…
Comment: Sam file Header problem
by
saifulislam99121
• 0
Thank you for your reply. I am not very much sure about this RG. Can you explain me a bit?
Comment: GRIDSS: the Genomic Rearrangement IDentification Software Suite
by
dario.garvan
▴ 520
It seems that Alexandrov's [structural variant and copy number signatures][1] estimated by the [SigProfiler software ecosystem][2] aren't c…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
GenoMax
142k
Then you may want to see if a program like `lastz` ([**LINK**][1]) may be useful. [1]: https://github.com/lastz/lastz
Comment: Collect dispersed executable files and run them by using bingo.
by
Ram
43k
What is the purpose of this tool? I have `~/bin` in my $PATH and I soft-link all executables I need to that location so why install a new t…
Comment: Merge clusters in Seurat UMAP
by
bk11
★ 2.4k
Can you try this? library(dplyr) seuratobj@meta.data <- seuratobj@meta.data %>% mutate(seurat_clusters = recode(seurat_clu…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
Thank you for the response but it does not change anything.
Comment: Merge clusters in Seurat UMAP
by
bk11
★ 2.4k
I have not tested but you could try something like below- seuratobj$seurat_clusters[seuratobj$seurat_clusters==5]=0 seuratobj$seur…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
I know about it, isn't there a simple C++ static binary?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
needle is great! but it does not handle sequences of 100k or so.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
by
txema.heredia
▴ 130
The point is that you need to feed the ambient algorithm a clustering list as input. This way, it checks for genes present in the soup vs g…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
swbarnes2
14k
Wait, so the magnitudes of the PCs are in the thousands? That's not normal for RNASeq.
Traffic: 1485 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6