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737 results • Page 3 of 15
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2
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8
replies
3.7k
views
Tool: Mirnakey - A Software Pipeline For The Analysis Of Microrna Deep Sequencing Data
mirna
updated 10 months ago by 43k • written 11.8 years ago by 100k
8
votes
8
replies
3.3k
views
Tool: pyGeno 1.2: Python package for Personalized Genomics and Proteomics
python SNP rna-seq dbSNP ensembl
updated 23 months ago by 43k • written 9.1 years ago by ▴ 220
7
votes
7
replies
4.7k
views
Tool: Variant Annotation, Analysis and Search Tool - VAAST2
VAAST2 VAAST
updated 10 months ago by 43k • written 10.1 years ago by 12k
2
votes
7
replies
2.7k
views
Tool: metaflagstat.py - painless bam/sam read flag counting
samtools bam
updated 10 months ago by 43k • written 9.7 years ago by 13k
6
votes
7
replies
3.1k
views
Tool: MutScan: detect and visualize target mutations by just scanning FastQ, 50X faster than normal pipelines
Mutation FastQ MutScan OpenGene
updated 10 months ago by 43k • written 7.2 years ago by ★ 2.5k
4
votes
7
replies
1.4k
views
Tool: Elloreas, a new genome assembler
Assembly next-gen
updated 11 months ago by 43k • written 3.9 years ago by ★ 1.2k
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
13
votes
7
replies
9.8k
views
Tool: Command-Line Software For Bigwig Data
bigwig
updated 11 months ago by 43k • written 10.5 years ago by ▴ 90
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
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
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
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 • 0 • written 7.0 years ago by 3.5k
2
votes
7
replies
2.9k
views
Tool: An online cute tool to query tumor-gene data from MSK-IMPACT project
MSK-IMPACT tumor mutation MSK
updated 10 months ago by 43k • written 7.0 years ago by ★ 2.5k
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
6
votes
7
replies
2.5k
views
Tool: Workflow for structural variants from long read sequencing data
structural-variation pacbio nanopore snakemake
updated 11 months ago by 43k • written 5.6 years ago by 47k
9
votes
7
replies
1.7k
views
Tool: miniDBG - a Jupyter notebook for teaching De Bruijn Graph assembly
python deBruijnGraph de_bruijn_graph assembly teaching
2.1 years ago by Michael 54k
5
votes
7
replies
3.7k
views
Tool: CircTools: Softwares for Discovering circRNA-microRNA Interactions from CLIP-Seq Datasets
circRNA CLIP-seq microRNA RNA-seq Interactome
updated 11 months ago by 43k • written 6.1 years ago by ▴ 860
28
votes
7
replies
11k
views
Tool: Quast Is A Convenient Tool For Assembly Evaluation
assembly quality
updated 10 months ago by 43k • written 11.2 years ago by ★ 1.3k
54
votes
7
replies
4.0k
views
6 follow
Tool: Looking For People That Would Try A Custom Genome Viewer That I Wrote For Bioinformatics
genome-viewer
updated 10 months ago by 43k • written 11.0 years ago by ▴ 40
3
votes
7
replies
1.4k
views
Tool: New method for protein secondary structure prediction
protein secondary-structure
updated 11 months ago by 43k • written 4.7 years ago by ▴ 180
27
votes
6
replies
16k
views
Tool: Bioawk - Fasta, Fastq, Sam, Bed, Gff Aware Awk Programming
awk
updated 10 months ago by 43k • written 11.9 years ago by 100k
18
votes
6
replies
4.9k
views
Tool: R code for ecological data analysis
next-gen R Metagenomics
updated 2.1 years ago by 43k • written 9.3 years ago by ★ 1.8k
13
votes
6
replies
5.2k
views
Tool: csvtk - a cross-platform, efficient, practical and pretty CSV/TSV toolkit
CSV Golang TSV
9 months ago by shenwei356 8.5k
4
votes
6
replies
5.8k
views
Tool: Fungal genome annotation
genome sequencing
updated 2.4 years ago by 43k • written 9.3 years ago by ▴ 90
8
votes
6
replies
3.8k
views
Tool: New ultraperformant version of SICER/epic: epic2
ChIP-Seq
updated 11 months ago by 43k • written 5.5 years ago by ▴ 110
2
votes
6
replies
3.4k
views
Tool: microbiomeMarker: microbiome biomarker analysis in R
stamp microbiome lefse
updated 11 months ago by 43k • written 3.9 years ago by ▴ 30
4
votes
6
replies
2.6k
views
Tool: How to find the Genes present in the sequence?
gene genome sequence
updated 22 months ago by 43k • written 9.1 years ago by ▴ 60
4
votes
6
replies
5.3k
views
Tool: NtSeq: JavaScript bioinformatics library for nucleotide sequence manipulation and analysis.
alignment JavaScript sequence
updated 2.1 years ago by 43k • written 9.3 years ago by ▴ 60
2
votes
6
replies
5.2k
views
Tool: Variantannotation Package (Bioconductor)
snp variant-annotation
updated 10 months ago by 43k • written 11.8 years ago by 20k
53
votes
6
replies
9.8k
views
8 follow
Tool: list of dockerized bioinformatics apps
docker
updated 2.3 years ago by 43k • written 9.6 years ago by ★ 3.6k
32
votes
6
replies
12k
views
Tool: FASTA and FASTQ tools
Cpp FASTA Python FASTQ
updated 16 months ago by 43k • written 9.0 years ago by ★ 2.3k
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
15
votes
6
replies
7.2k
views
Tool: Sambamba: High Performance Alternative For Samtools And Picard For Indexing, Sorting And Merging Bam Files
sambamba bam samtools
updated 10 months ago by 43k • written 10.7 years ago by ★ 5.3k
7
votes
6
replies
6.5k
views
Tool: PlantTFDB and PlantRegMap: Plant Transcription Factor Database and Plant Regulation Data and Analysis Platform
transcriptional-regulation enrichment binding-site
updated 11 months ago by 43k • written 7.6 years ago by ▴ 80
13
votes
6
replies
4.9k
views
Tool: GAWN - Genome Annotation Without Nightmares
genome-annotation
updated 11 months ago by 43k • written 6.8 years ago by 11k
6
votes
6
replies
4.8k
views
Tool: Reading/ Writing FASTA files in Java
FASTA Java
updated 10 months ago by 43k • written 9.4 years ago by • 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 43k • written 3.3 years ago by • 0
2
votes
6
replies
2.1k
views
Tool: Primer design shiny app
SNP sequencing
updated 10 months ago by 43k • written 7.6 years ago by ▴ 10
4
votes
6
replies
4.4k
views
Tool: StrainControl Laboratory Manager software
LIMS Lab-management Lab-database
updated 2.1 years ago by 43k • written 9.3 years ago by ▴ 20
1
vote
6
replies
2.1k
views
Tool: CSBB [Computational Suite For Biologists and Bioinformaticians]
perl RNA-Seq R
updated 13 months ago by 43k • written 7.9 years ago by • 0
7
votes
6
replies
5.1k
views
Tool: mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
depth-of-coverage exome WGS
updated 11 months ago by 43k • written 6.3 years ago by 24k
4
votes
6
replies
2.7k
views
Tool: Bamchop: Efficient Digest Of High-Throughput Sequencing Data In A Reproducible Report
bam
updated 10 months ago by 43k • written 10.7 years ago by 22k
5
votes
6
replies
4.6k
views
Tool: Filter VCFs with ExAC data
next-gen SNVs exome filter
updated 2.3 years ago by 43k • written 9.5 years ago by ▴ 40
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 43k • written 5.1 years ago by ▴ 80
13
votes
6
replies
3.0k
views
Tool: Open source bioinformatics tools: Blaster, Primer Factory, Labtools
primer blast alignment bowtie
updated 2.4 years ago by 43k • written 9.4 years ago by ▴ 110
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
19
votes
5
replies
8.0k
views
Tool: deepTools: user-friendly tools for the normalization and visualization of deep-sequencing data
Visualisation RNA-Seq QC ChIP-Seq
updated 10 months ago by 43k • written 10.0 years ago by ▴ 670
8
votes
5
replies
4.7k
views
Tool: GFF3 to EMBL converter
gff3 embl
updated 11 months ago by 43k • written 6.7 years ago by 8.6k
5
votes
5
replies
5.0k
views
Tool: Mutect: Accurate Identification Of Somatic Point Mutations
mutect
updated 10 months ago by 43k • written 12.1 years ago by 11k
2
votes
5
replies
985
views
Tool: Latest release of NCBI Magic-BLAST now available
BLAST NCBI Magic-BLAST
updated 22 months ago by 142k • written 23 months ago by ▴ 410
737 results • Page 3 of 15
Recent Votes
The Biostar Herald for Monday, May 20, 2024
Answer: Generating Group/Cluster Lists from fastq files
The Biostar Herald for Monday, May 20, 2024
ClusterProfiler : What is GeneRatio and BgRatio?
A: ClusterProfiler : What is GeneRatio and BgRatio?
A: ClusterProfiler : What is GeneRatio and BgRatio?
C: Cleaning RNA-Seq data from rRNA
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Recent Replies
Comment: Filter Genome for Specific Sites by Pierre Lindenbaum 161k
> My sites are in an Excel file right now ![enter image description here][1] <!-- was an American educator and academic administrator…
Comment: Filter Genome for Specific Sites by GenoMax 142k
> I have a list of ~1,300 single bp sites Convert your file to plain text [**BED format**][1] (three fields required). Use `bedtools slo…
Comment: How to generate an Upset plot in R to plot the shared variants between cell free by sainavyav22 • 0
It worked, Thank you very much!
Comment: What marks a De-Novo Genome assembly as FAILED? by dthorbur ★ 2.0k
I'm unsure you'll be able to identify whole chromosomes that are not core from illumina reads alone. That might be easier to do with a micr…
Answer: Error in using BioSampleParser tool: subscript out of bounds by Mohamed Samir ▴ 20
Dear marco, We need to ask ourselves why it is not working for all bioprojects ? I have looked into this, and observed that as long as the…
Comment: Why most genes have high padj values by Ram 43k
You ***want*** ~3000 DE genes?<a href="" title="Text added because biostars parser needs it"></a>
Answer: Generating Group/Cluster Lists from fastq files by GenoMax 142k
> I was hoping to just do this in galaxy This is not a galaxy option but `clumpify.sh ` from BBMap suite can cluster sequences/dedupe th…
Comment: Practical Haplotype Graph v2 not finding correct paths by beantkapoor16 ▴ 10
Hello, just wanted to check in if the code has been fixed yet? Thank you.
Comment: Super ehancers by jared.andrews07 ★ 16k
Based on the [source code](https://bitbucket.org/young_computation/rose/src/feb35cb1d9556a76f8ac1f51521539bb30651343/ROSE_utils.py?at=maste…
Comment: HGVS Nomenclature of Multiple Indels found in Cis by Ram 43k
They're not addressing the actual question, just saying something tangentially related. It looks like their understanding of both consensus…
Comment: Super ehancers by Oburah • 0
Hello, i encountered this problem when running ROSE, Do anyone know how to solve it? python2.7 ROSE_main.py -g HG38 -i /home/hesborn/…
Answer: How to generate an Upset plot in R to plot the shared variants between cell free by zx8754 11k
Try this example: library(UpSetR) #example input, 4 samples, 250 variants set.seed(1); d <- data.frame(matrix(sample…
Answer: Illumina methylation EPIC V2 array by fu_entomology ▴ 40
We have been using SeSAMe, it works well for the most part. They have an enrichment tool called KnowYourCG. You can check it out their vign…
Answer: How to find identical sequences in genome fasta file (by Python or any possible by GenoMax 142k
> My final purpose are find and remove any identical sequences present in my genome fasta file. You can use `clumpify.sh` from BBMap suite…
Comment: GO analysis: Indicate genes corresponding to the pathway by marco.barr ▴ 130
I think you have set a filter to get these pahways upstream from the DEG results. You should extract the IDs or names of the genes that you…
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