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515 results • Page
2 of 11
Sort: Rank
Rank
Views
Votes
Replies
5
votes
3
replies
886
views
Tool:
Experiment Generator
gpt
updated 11 months ago by
LauferVA
4.2k • written 11 months ago by
Sasha
▴ 850
362
votes
82
replies
145k
views
35 follow
Tool:
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel
next-gen
ngs
updated 8 weeks ago by
jena
▴ 290 • written 11.3 years ago by
ole.tange
★ 4.4k
4
votes
0
replies
943
views
Tool:
PyComplexHeatmap: a Python package to visualize multimodal genomics data
visualization
Python
ComplexHeatmap
PyComplexHeatmap
6 weeks ago by
Wubin
▴ 40
9
votes
23
replies
9.9k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
15 days ago by
vytarasov
▴ 180
1
vote
0
replies
791
views
Tool:
Mabs, a parameter optimizer for Hifiasm and Flye
assembly
8 months ago by
shelkmike
★ 1.2k
2
votes
4
replies
1.1k
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
▴ 850
4
votes
2
replies
1.3k
views
Tool:
Introducing Cramino: a *fast* QC tool for long reads
long-read
nanopore
pacbio
updated 7 weeks ago by
Ram
44k • written 18 months ago by
WouterDeCoster
47k
28
votes
4
replies
15k
views
Tool:
Plotting GSEA output in R
RNA-Seq
javaGSEA
GSEA
updated 11 months ago by
Ram
44k • written 7.8 years ago by
thomaskuilman
▴ 850
25
votes
19
replies
8.3k
views
10 follow
Tool:
pathfindR - Enrichment Analysis using Active Subnetworks
subnetwork
R
pathway-enrichment
updated 11 months ago by
Ram
44k • 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
44k • 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
44k • 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
44k • written 7.0 years ago by
bernatgel
★ 3.4k
2
votes
0
replies
597
views
Tool:
Introducing ElasticBLAST – Run bigger BLAST searches faster on the Cloud
ElasticBLAST
BLAST
NCBI
updated 11 months ago by
Ram
44k • written 2.2 years ago by
PeterC_NCBI
▴ 420
231
votes
38
replies
147k
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
44k • 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
44k • 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
44k • written 6.0 years ago by
tomastokar
▴ 50
2
votes
6
replies
3.5k
views
Tool:
microbiomeMarker: microbiome biomarker analysis in R
stamp
microbiome
lefse
updated 11 months ago by
Ram
44k • written 3.9 years ago by
yiluheihei
▴ 30
5
votes
8
replies
7.1k
views
6 follow
Tool:
Converting MUMmer snps file to a real VCF file
VCF
mummer
SNP
updated 11 months ago by
Ram
44k • written 4.8 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
44k • 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
44k • 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
11 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
44k • 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
44k • written 3.7 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
44k • written 10.7 years ago by
arnaud.desfeux
▴ 450
21
votes
14
replies
9.6k
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
44k • 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
44k • written 3.6 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
44k • 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 7.1 years ago by
mikhail.shugay
3.5k
1
vote
0
replies
604
views
Tool:
Super easy to use free paper retrieval artifact: PyPubMed
python
pubmed
software
updated 11 months ago by
Ram
44k • written 3.0 years ago by
Novogene
▴ 420
0
votes
0
replies
705
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
44k • 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
44k • 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
44k • written 5.4 years ago by
slcrick
▴ 260
2
votes
1
reply
783
views
Tool:
Bioinformatics Programming Package
Package
updated 11 months ago by
Ram
44k • 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 7 months ago by
GenoMax
142k • written 5.2 years ago by
Phil Ewels
★ 1.4k
2
votes
0
replies
869
views
Tool:
New location tracking tool for SARS-CoV-2 variant surveillance
sars-cov-2
variant
covid-19
updated 11 months ago by
Ram
44k • 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 11 months ago by
Ram
44k • written 4.4 years ago by
Juke34
8.6k
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
44k • 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
44k • 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
44k • written 3.8 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
44k • written 3.3 years ago by
Jennifer Pham
▴ 450
0
votes
0
replies
675
views
Tool:
MultiLink Analysis: Brain Network Comparison via Sparse Connectivity Analysis
networks
neuroscience
connectome
brain
updated 11 months ago by
Ram
44k • written 3.3 years ago by
alex.crimi
• 0
1
vote
0
replies
686
views
Tool:
BiOkeanos - the largest(*) biomedical database catalogue and discovery tool
database
catalogue
data
updated 11 months ago by
Ram
44k • written 3.3 years ago by
ellimilial
▴ 20
0
votes
0
replies
847
views
Tool:
Analyze & Visualize Nephele Microbiome Results Using MicrobiomeDB
microbiome
sequence
updated 11 months ago by
Ram
44k • 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
44k • 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
44k • written 3.7 years ago by
Juke34
8.6k
0
votes
0
replies
635
views
Tool:
Cytoscape Network analysis
software-error
cytoscape
updated 11 months ago by
Ram
44k • 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
44k • 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
44k • written 5.9 years ago by
chen
★ 2.5k
4
votes
2
replies
1.1k
views
Tool:
Alternate the wild type and mutant of SARS-CoV-2 N501Y
SNP
updated 11 months ago by
Ram
44k • written 3.4 years ago by
Jiyao Wang
▴ 370
24
votes
26
replies
3.7k
views
Tool:
ClinCNV: CNV detection from short reads
variant-calling
cna
cnv
updated 11 months ago by
Ram
44k • written 4.6 years ago by
German.M.Demidov
★ 2.9k
515 results • Page
2 of 11
Recent Votes
C: The Biostar Handbook. A bioinformatics e-book for beginners.
Answer: Error with BiocParallel. No barcodes files found
Error with BiocParallel. No barcodes files found
Comment: How do we do quantification using stringtie merge option for all the merged samp
Answer: bcftools view error: the tag "mis" is not defined in the VCF header
Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
Search within posts based on tags using the Biostars API
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Recent Awards •
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Recent Replies
Comment: How do we do quantification using stringtie merge option for all the merged samp
by
Varsha
• 0
Thank you for the detailed explanation.
Answer: How can run cd-hit-est with a clstr threshold less than 0.8?
by
Asaf
10k
For future reference The 0.8 identity threshold for EST (nucleotides) is hardcoded. However, there's an option to use `-D` (distance) in…
Answer: Tools for chromosomal aneuploidy detection
by
a.alnawfal.1992
▴ 260
As far as I know, all the tools utilised control group to compute the z score for chromosomal aneuploidy. but is your goal detect chromosom…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2
by
Sara
▴ 30
I used Seurat, and in Seurat, I have gene names (which some are with gene-symbols and some with ENSG ids). Then I did Pseudobulk. how can …
Comment: How to decrease the motif score?
by
ATpoint
82k
So you scan the entire genome and got nothing significant? Is that the issue?
Comment: perl Error - needLargeMem Bigwig
by
b.contreras.moreira
▴ 200
A quick search suggests the problem is your empty input file? See <https://biostar.galaxyproject.org/p/6794>
Comment: Invalid CIGAR after using bam clipOverlap
by
MboiTui
▴ 20
ooh good pickup. Might not be the problem but definitely not helping. Will re-run with streamlined workflow and with double quotes and see …
Comment: Invalid CIGAR after using bam clipOverlap
by
Pierre Lindenbaum
162k
may be not the problem but why this ` RG:Z:H7J22DRX3.${lane}-1C23074F ` in the RG. you're using single quotes with bwa-mem and it won't …
Comment: Invalid CIGAR after using bam clipOverlap
by
MboiTui
▴ 20
Hello Pierre, Thanks for your reply and insight. with samtools view | grep using the erroneous CIGAR string I get: A00152:841:H7J22D…
Comment: Invalid CIGAR after using bam clipOverlap
by
Pierre Lindenbaum
162k
please, show us the following output: samtools view "${Ind1}_sorted_dup.bam" | grep -F "A00152:841:H7J22DRX3:2:1112:5267:11397" Furth…
Comment: Failed to download data from EBI with ascp
by
孝中
• 0
Hi, have you found the solution to this problem?
Comment: samtools write-index
by
R.L.
• 0
Oh God, thank you so much for helping me in both platforms! I am gonna upgrade my samtools to stay tracked with you and your team! Thank yo…
Answer: How to add Ensembl ids after Pseudobulk analysis by DESeq2
by
jared.andrews07
★ 17k
Go back to your original counts matrix or input data and assign consistent IDs during its generation.
Answer: Facing problem with single cell rna seq annotation using singleR
by
jared.andrews07
★ 17k
A few things. >(1)What did i do wrong here? SingleR will annotate each cell with whatever it's most similar to in the reference datas…
Comment: Harmony integration group.by.var parameter
by
jared.andrews07
★ 17k
Couldn't tell you, I avoid Seurat like the plague.
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