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515 results • Page
2 of 11
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Rank
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Votes
Replies
0
votes
0
replies
505
views
Tool:
Easy API For Running Bioinformatics Jobs Via Python In The Cloud
api
execution
12 months ago by
Sasha
▴ 850
362
votes
82
replies
144k
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
931
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
9.9k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
11 days ago by
vytarasov
▴ 180
1
vote
0
replies
789
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 6 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
8.2k
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
▴ 410
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
3.4k
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
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
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 3.6 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
44k • 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
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 7.0 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
44k • written 3.0 years ago by
Novogene
▴ 420
0
votes
0
replies
704
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
779
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
867
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 3.7 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
44k • written 3.3 years ago by
Jennifer Pham
▴ 450
0
votes
0
replies
674
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
685
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
844
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 3.6 years ago by
Juke34
8.6k
0
votes
0
replies
634
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: Classifying normal vs cancer tissues from mutational data
Classifying normal vs cancer tissues from mutational data
Pymol Scripting Help
A: Not sure if pipe from bowtie2 to samtools is working?
Comment: FastQC interpretation - 16S sequencing
Comment: FastQC interpretation - 16S sequencing
Answer: vg autoindex seems stuck after a week of running
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Comment: Trimmomatic running but files containing purged reads are empty
by
GenoMax
142k
> Why is trimmomatic not removing any reads? It is not mandatory that your data have extraneous/adapter sequence. If no extraneous sequenc…
Comment: FastQC interpretation - 16S sequencing
by
GenoMax
142k
Since a specific region is being amplified it is expected that many of the library fragments will have identical sequences. Thus the low nu…
Comment: FastQC interpretation - 16S sequencing
by
Christopher
• 0
@genomax Thank you so much for replying. I was quite unsure about the qualities. One more question. There is no problem within nucleotide d…
Comment: FastQC interpretation - 16S sequencing
by
GenoMax
142k
> My specific question is about the feasibility of per base sequence content analysis and whether I should be concerned about a particular …
Comment: How to get the ratio of allele counts from GATK derived VCF file?
by
anikcropscience
▴ 230
But I used the same bam files in both freebayes and GATK. Even the overlapping SNPs from both software are giving different estimates in te…
Comment: How to get the ratio of allele counts from GATK derived VCF file?
by
Pierre Lindenbaum
162k
may be downsampling(?), QC failing reads ?
Comment: How to get the ratio of allele counts from GATK derived VCF file?
by
anikcropscience
▴ 230
Thank you. However, I extracted the AD for each SNP that gives two numbers separated by a comma. I guess the first one is for reference and…
Answer: How to get the ratio of allele counts from GATK derived VCF file?
by
Pierre Lindenbaum
162k
> However, I am doing SNP calling using GATK, but there is no such information field for reference and alternate allele counts. it's in …
Comment: samtools write-index
by
GenoMax
142k
> The index file is older than the data file: alignment.sorted.bam.bai I don't think that warning is going to cause any issues. Not sure w…
Comment: samtools write-index
by
Pierre Lindenbaum
162k
can you please retry, but add rm -vf alignment.sorted.bam.bai before invoking minimap2. And `-o alignment.sorted.bam` should be enoug…
Answer: from CRAM to fastq
by
Pierre Lindenbaum
162k
if the CRAM/BAM is paire-end, it **must** be sorted on query name using samtools collate https://x.com/lh3lh3/status/1132756684789768202 …
Comment: from CRAM to fastq
by
machaalani29
• 0
one of the issues is that I am not very sure how the sequencing was done, but I think it was single end. any suggestions hoot do that?
Comment: from CRAM to fastq
by
machaalani29
• 0
the option -c is to compress the file
Comment: from CRAM to fastq
by
GenoMax
142k
Possibly. You appear to have written the data to a single file (in case it was paired-end to begin with). Check to make sure secondary alig…
Comment: converting transcript IDs (Ensembl) to gene symbols in R
by
GenoMax
142k
https://www.biostars.org/u/18990/ : Please do not delete threads that have received a comment/answer.
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