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521 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 5 weeks ago by
jena
▴ 290 • written 11.2 years ago by
ole.tange
★ 4.4k
4
votes
0
replies
881
views
Tool:
PyComplexHeatmap: a Python package to visualize multimodal genomics data
visualization
Python
ComplexHeatmap
PyComplexHeatmap
23 days ago by
Wubin
▴ 40
9
votes
22
replies
9.7k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
10 months ago by
vytarasov
▴ 180
1
vote
0
replies
780
views
Tool:
Mabs, a parameter optimizer for Hifiasm and Flye
assembly
7 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 5 months ago by
mavy
▴ 10 • written 17 months ago by
Sasha
▴ 840
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
Ram
43k • written 18 months ago by
WouterDeCoster
47k
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
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
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 8.1 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
2
votes
0
replies
592
views
Tool:
Introducing ElasticBLAST – Run bigger BLAST searches faster on the Cloud
ElasticBLAST
BLAST
NCBI
updated 10 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 10 months ago by
Ram
43k • written 11.2 years ago by
Malachi Griffith
19k
5
votes
2
replies
2.4k
views
Tool:
eLabFTW: a free and open source electronic lab notebook
elabftw
free-open-source-software
php
updated 10 months ago by
Ram
43k • written 4.6 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 10 months ago by
Ram
43k • written 5.9 years ago by
tomastokar
▴ 50
2
votes
6
replies
3.4k
views
Tool:
microbiomeMarker: microbiome biomarker analysis in R
stamp
microbiome
lefse
updated 10 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 10 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 10 months ago by
Ram
43k • written 6.2 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 10 months ago by
Ram
43k • written 5.2 years ago by
Kevin Blighe
87k
10
votes
5
replies
2.4k
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 10 months ago by
Ram
43k • written 3.2 years ago by
bigmawen
▴ 430
3
votes
5
replies
2.7k
views
Tool:
Extend 3' UTR of a GTF file
annotation
python
RNA-Seq
GTF
updated 10 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 10 months ago by
Ram
43k • written 10.6 years ago by
arnaud.desfeux
▴ 450
21
votes
14
replies
9.4k
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 10 months ago by
Ram
43k • written 3.4 years ago by
poisonAlien
★ 3.2k
9
votes
7
replies
2.9k
views
Tool:
DiffBind 3.0: Extensive updates in Bioconductor 3.12
DiffBind
ChIP-Seq
diffbind
ATAC-seq
chipseq
updated 10 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 10 months ago by
Ram
43k • written 4.5 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 11 weeks ago by
blid11
• 0 • written 7.0 years ago by
mikhail.shugay
3.5k
1
vote
0
replies
596
views
Tool:
Super easy to use free paper retrieval artifact: PyPubMed
python
pubmed
software
updated 10 months ago by
Ram
43k • written 2.9 years ago by
Novogene
▴ 420
0
votes
0
replies
698
views
Tool:
IPC 2.0: prediction of isoelectric point and pKa dissociation constants
deep-learning
isoelectric-point
2D-PAGE
pKa
updated 10 months ago by
Ram
43k • written 3.0 years ago by
Lukasz Kozlowski
• 0
8
votes
6
replies
5.8k
views
Tool:
chromoMap- R package for Interactive visualization and Annotation of chromosomes or regions of any living organism.
annotation
R
genome
visualization
updated 10 months ago by
Ram
43k • written 5.0 years ago by
lakshayanand15
▴ 80
13
votes
14
replies
6.1k
views
9 follow
Tool:
open-cravat: variant annotation tool
open-cravat
updated 10 months ago by
Ram
43k • written 5.4 years ago by
slcrick
▴ 260
2
votes
1
reply
774
views
Tool:
Bioinformatics Programming Package
Package
updated 10 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
857
views
Tool:
New location tracking tool for SARS-CoV-2 variant surveillance
sars-cov-2
variant
covid-19
updated 10 months ago by
Ram
43k • written 3.1 years ago by
ehaag
▴ 20
12
votes
5
replies
6.1k
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 11 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 10 months ago by
Ram
43k • written 3.2 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 10 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 10 months ago by
Ram
43k • written 3.7 years ago by
Kevin Blighe
87k
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 10 months ago by
Ram
43k • written 3.2 years ago by
Jennifer Pham
▴ 450
0
votes
0
replies
669
views
Tool:
MultiLink Analysis: Brain Network Comparison via Sparse Connectivity Analysis
networks
neuroscience
connectome
brain
updated 10 months ago by
Ram
43k • written 3.2 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 10 months ago by
Ram
43k • written 3.2 years ago by
ellimilial
▴ 20
0
votes
0
replies
837
views
Tool:
Analyze & Visualize Nephele Microbiome Results Using MicrobiomeDB
microbiome
sequence
updated 10 months ago by
Ram
43k • written 3.2 years ago by
karlynn.noble
▴ 60
22
votes
20
replies
4.8k
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 10 months ago by
Ram
43k • written 5.5 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 10 months ago by
Ram
43k • written 3.6 years ago by
Juke34
8.6k
0
votes
0
replies
630
views
Tool:
Cytoscape Network analysis
software-error
cytoscape
updated 10 months ago by
Ram
43k • written 3.2 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 10 months ago by
Ram
43k • written 3.3 years ago by
jayeshkumarsundaram
• 0
11
votes
2
replies
7.0k
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 10 months ago by
Ram
43k • written 5.8 years ago by
chen
★ 2.5k
521 results • Page
2 of 11
Recent Votes
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
A: After read mapping, count exons or genes?
After read mapping, count exons or genes?
Merging a large number of VCF files
A: Merging a large number of VCF files
A: pulling snps from vcf file using ids
pulling snps from vcf file using ids
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Recent Awards •
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SHN
▴ 40
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Rob
▴ 170
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GenoMax
142k
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▴ 750
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Recent Replies
Comment: filtering before dada2
by
GenoMax
142k
> I encountered a significant decrease in the percentage of merged reads. You can check with `bbmerge.sh` from BBMap suite to see how many…
Comment: HCL database download
by
GenoMax
142k
Isn't the download link available above the plot: http://bis.zju.edu.cn/HCL/data/DGE/Adult-Transverse-Colon1_dge.txt.gz
Comment: fastq screen aligner no specified.
by
GenoMax
142k
You need to change this configuration file to point it to the location where the aligner executable can be found. So as an example followi…
Answer: Design matrix Differential expression analysis
by
Gordon Smyth
★ 7.1k
The expression levels do not change but the way that you have parametrized the expression levels does change. The two design matrices give…
Comment: The GDC Legacy Archive is retiring soon.
by
lcordeiro
▴ 40
Hi Zhenyu, do you happen to know how I can download metadata for some of the legacy files? I downloaded several IDATs from the legacy data …
Answer: Force PLINK2 to neglect chrX as the sex chromosome
by
chrchang523
10k
(cross-posted from https://groups.google.com/g/plink2-users/c/Qphx_6BpPII ) You need to use --chr-set, not --allow-extra-chr, to specify…
Answer: Easy way to find out which allele is minor allele from bed file?
by
chrchang523
10k
This question does not make sense. If you care about allele-order "information [being] lost in downstream applications", REF/ALT is the ob…
Answer: visualize GSEA
by
bk11
★ 2.4k
I have made some edits in your code basically changing the position of text and commented out the line `data$text_pos <- ifelse(data$NES > …
Comment: Differential Expression Analysis using DESeq2 in R
by
swbarnes2
14k
Pictures of code are useless. You were told to paste the code and use the 0101 button. Can you explain why you decided not to do that? If…
Comment: 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…
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