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736 results • Page 3 of 15
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13
votes
7
replies
4.2k
views
Tool: I-PV: a CIRCOS module for interactive protein sequence visualization
interactive javascript circos sequence
updated 21 months ago by 43k • written 8.6 years ago by ★ 1.2k
12
votes
3
replies
3.1k
views
Tool: The Biopieces Are A Collection Of Bioinformatics Tools
sequence
updated 10 months ago by 43k • written 11.3 years ago by 9.7k
12
votes
3
replies
2.8k
views
Tool: Hiplot: a simple and user-friendly visualization platform for scientific data
R microbial RNA-Seq visualization
updated 11 months ago by 43k • written 3.8 years ago by ▴ 130
12
votes
6
replies
3.5k
views
Tool: Variant annotation and filtration server ALAPY Genome Explorer (AGx)
vcf variant-annotation variant-interpretation
updated 10 months ago by 43k • written 7.0 years ago by ★ 2.8k
12
votes
1
reply
2.7k
views
Tool: iStack: an R solution for plotting stacked bars using custom icons
R
updated 11 months ago by 43k • written 5.4 years ago by ▴ 150
12
votes
7
replies
3.2k
views
Tool: Chromozoom: The Genome Browser That Lets You Fly!
genome-browser browser
updated 10 months ago by 43k • written 11.2 years ago by 100k
12
votes
4
replies
1.1k
views
Tool: BBTools 39.03 released!
BBTools BBMap
7 months ago by Brian Bushnell 20k
12
votes
5
replies
3.6k
views
Tool: Kitten - A DNA Sequence Dereplicator & Cluster Viewer (GUI)
dereplication sequence nextgen clustering
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 790
12
votes
5
replies
3.6k
views
Tool: biomartian enables querying BioMart from the command line - now all Python!
biomart
updated 19 months ago by 43k • written 8.8 years ago by ▴ 960
12
votes
5
replies
6.2k
views
Tool: AGAT - Another Gff/Gtf Analysis Toolkit
gff gtf
updated 10 months ago by 43k • written 4.4 years ago by 8.6k
12
votes
0
replies
4.8k
views
Tool: UMI-Tools 0.5, now with tools for cell barcoded scRNA-seq
UMI RNA-Seq single-cell
updated 11 months ago by 43k • written 6.7 years ago by 19k
12
votes
8
replies
3.2k
views
Tool: BioBit: Global bioinformatics chat
communication
updated 13 months ago by 43k • written 7.9 years ago by ▴ 90
12
votes
9
replies
7.8k
views
Tool: gogadget: an R package for go analysis visualization and interpretation
goseq R RNA-Seq gogadget
updated 11 months ago by 43k • written 7.8 years ago by 8.3k
11
votes
12
replies
4.9k
views
Tool: Mapsembler2 targeted micro assembly and visualization of the local assembly graph
minia mapsembler next-gen Assembly
updated 2.1 years ago by 43k • written 9.8 years ago by ▴ 900
11
votes
2
replies
13k
views
Tool: Multiplex PCR Primer Design Tools
multiplex-PCR
updated 11 months ago by 43k • written 6.7 years ago by ★ 9.4k
11
votes
10
replies
2.3k
views
Tool: [Crushing the bureaucracy in bioinformatics] Introducing Skymap-JupyterHub: accessing and utilizing reprocessed expression/ allelic read count profil…
SNP RNA-Seq ChIP-Seq
updated 11 months ago by 43k • written 5.8 years ago by ▴ 300
11
votes
7
replies
6.2k
views
Tool: RNA Modification Database and Epitranscriptome Sequencing Data
Epitranscriptome m5C m6A RNA-modification m1A
updated 20 months ago by 43k • written 8.6 years ago by ▴ 860
11
votes
2
replies
2.7k
views
Tool: Open Targets batch search, your list of human genes matched to our disease associations
Disease Drug Open-Targets
updated 12 months ago by 43k • written 7.0 years ago by ★ 5.2k
11
votes
2
replies
781
views
Tool: Pipeline Generator
gpt
updated 9 months ago by 4.2k • written 9 months ago by ▴ 850
11
votes
3
replies
4.6k
views
Tool: Dgidb - Mining The Druggable Genome
dgidb drug-gene-interaction
updated 10 months ago by 43k • written 10.6 years ago by 20k
11
votes
3
replies
2.8k
views
Tool: Sequence Database curator
sequence fastq sequencing blast
updated 11 months ago by 43k • written 7.3 years ago by ▴ 110
11
votes
2
replies
5.3k
views
Tool: ChIPQC: a package for assessing quality of ChIP-seq samples and experiments
quality-control quality-assessment ChIP-Seq
updated 10 months ago by 43k • written 10.1 years ago by ★ 2.0k
11
votes
14
replies
6.5k
views
6 follow
Tool: [share] Script to bulk retrieve DNA sequences by protein IDs from GenBank
python genbank sequence cds protein
updated 2.3 years ago by 43k • written 9.5 years ago by ▴ 130
11
votes
5
replies
2.6k
views
Tool: A resource with diverse databases and tools for SARS-CoV-2 (COVID-19) bioinformatics -- Updates
SARS-CoV-2 Corona Databases COVID-19
updated 11 months ago by 43k • written 4.2 years ago by ▴ 270
11
votes
0
replies
3.0k
views
Tool: Pyblue: A Simple Tool To Generate Data/Code Oriented Static Web Sites (version 2.0 released)
pyblue
updated 10 months ago by 43k • written 10.8 years ago by 100k
11
votes
2
replies
1.9k
views
Tool: Tools, Resources, Training material from ISMB/ECCB, BOSC 2017
BOSC ISMB Resources ECCB
updated 12 months ago by 43k • written 6.8 years ago by 7.1k
11
votes
1
reply
4.8k
views
Tool: Ideogram.js: a JavaScript library for chromosome visualization
javascript chromosome visualization ideogram
updated 11 months ago by 43k • written 6.2 years ago by ▴ 120
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 43k • written 5.9 years ago by ★ 2.5k
10
votes
12
replies
1.9k
views
Tool: PanDepth, an ultra-fast and efficient genomic tool for coverage calculation
bam paf depth cram coverage
3 months ago by Huiyang ▴ 190
10
votes
1
reply
7.5k
views
Tool: Comb-P: Combining Spatially Correlated P-Values
methylation
updated 10 months ago by 43k • written 11.6 years ago by 24k
10
votes
2
replies
7.5k
views
Tool: fastp, the ultra-fast FASTQ preprocessing tool, is now on BioConda
fastp
updated 14 months ago by 43k • written 6.4 years ago by ★ 2.5k
10
votes
0
replies
5.8k
views
Tool: Shell utilities for QC of FASTQ/FASTA files (based on perl one-liners)
PERL GNUPLOT FASTA FASTQ FastQC
updated 10 months ago by 43k • written 10.1 years ago by ★ 1.8k
10
votes
3
replies
6.3k
views
Tool: GenVisR: Genomic Visualizations in R
visualization genomic RNA-Seq genvisr
updated 11 months ago by 43k • written 7.9 years ago by 20k
10
votes
6
replies
5.7k
views
Tool: Shell script to automate trimmomatic for multiple samples
bash shell trimmomatic
updated 11 months ago by 43k • written 5.0 years ago by 5.8k
10
votes
8
replies
1.9k
views
6 follow
Tool: "bioalcidae, samjs and vcffilterjs" published in bioinformatics.
jvarkit bam vcf javascript java
updated 11 months ago by 43k • written 6.5 years ago by 161k
10
votes
1
reply
1.5k
views
Tool: fastp 0.23.0 released, runs 2x faster, and generates reproducible outputs.
FASTQ
updated 2.6 years ago by 142k • written 2.6 years ago by ★ 2.5k
10
votes
0
replies
2.7k
views
Tool: Real Time Programming for Bioinformatics (and for fun)
coderscrowd collaborative-editor
updated 14 months ago by 43k • written 9.8 years ago by ▴ 810
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
10
votes
2
replies
2.1k
views
Tool: Onezoom For Viewing Large Phylogenetic Tree Data
phylogeny
updated 10 months ago by 43k • written 11.6 years ago by 11k
9
votes
2
replies
3.9k
views
Tool: Patch ERCC spike sequences to get their real 5-prime ends.
spikes ERCC CAGE
updated 21 months ago by 43k • written 8.4 years ago by ★ 2.9k
9
votes
1
reply
7.0k
views
Tool: Rsem: Accurate Transcript Quantification From Rna-Seq Data With Or Without A Reference Genome
rna-seq RSEM
updated 10 months ago by 43k • written 11.7 years ago by 100k
9
votes
12
replies
4.6k
views
Tool: fastp v0.9 released: an all-in-one FASTQ preprocessor (QC, adapters, trimming, quality filtering / cutting, splitting output ... )
fastq fastp open-source
updated 11 months ago by 43k • written 6.6 years ago by ★ 2.5k
9
votes
8
replies
3.8k
views
6 follow
Tool: NCBI-SRA File Downloader
NCBI sra sequence
updated 14 months ago by 43k • written 8.7 years ago by ▴ 50
9
votes
9
replies
4.7k
views
Tool: pyCirclize - Circular visualization in Python
visualization circos matplotlib genome python
updated 9 months ago by • 0 • written 17 months ago by ▴ 150
9
votes
23
replies
9.8k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
7 days ago by vytarasov ▴ 180
9
votes
7
replies
3.6k
views
Tool: metaViC: Virus metagenomics pipeline for unknown host or in absence of a host genome
Assembly metagenomics ngs
updated 11 months ago by 43k • written 7.7 years ago by 5.3k
9
votes
4
replies
2.7k
views
Tool: Compareads: Comparing Huge Metagenomic Experiments
metagenomics denovo next-gen
updated 10 months ago by 43k • written 11.3 years ago by ▴ 180
9
votes
2
replies
3.8k
views
Tool: BioPandas - Working with molecular structures in pandas DataFrames
protein-structure protein-data-bank pdb
updated 21 months ago by 43k • written 8.5 years ago by ▴ 150
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 43k • written 3.6 years ago by ★ 2.0k
9
votes
4
replies
6.0k
views
Tool: BPGA - Bacterial Pan Genome Analysis pipeline
sequence genome comparative-genomics bacteria
updated 11 months ago by 43k • written 8.0 years ago by ▴ 80
736 results • Page 3 of 15
Recent Votes
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
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Popular Question to Muhammad • 0
Popular Question to synat.keam ▴ 100
Scholar to jv ★ 1.8k
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Recent Replies
Answer: Checking chromosome builds for genotyping data by Muhammad • 0
Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors) by nguyenn6 • 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed by anton.i.petrov • 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp by analyst ▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by GenoMax 142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R by 1769mkc ★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks by ATpoint 82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner by Joe 21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression? by Gordon Smyth ★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF) by aidangcruickshank ▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data? by Ngrin • 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
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