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737 results • Page 3 of 15
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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
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 43k • written 4.8 years ago by ★ 3.6k
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
5.8k
views
Tool: Fungal genome annotation
genome sequencing
updated 2.4 years ago by 43k • written 9.3 years ago by ▴ 90
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
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 10.6 years ago by ★ 5.3k
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
9
votes
5
replies
2.9k
views
Tool: DiscoSnp becomes DiscoSnp++
indels discoSnp gatb SNP
updated 18 months ago by 43k • written 9.3 years ago by ▴ 900
8
votes
5
replies
2.9k
views
Tool: Sequence filtration tool
fasta sequence filter
updated 11 months ago by 43k • written 7.2 years ago by ▴ 110
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
737 results • Page 3 of 15
Recent Votes
C: Cleaning RNA-Seq data from rRNA
Answer: How to find identical sequences in genome fasta file (by Python or any possible
Merging/Concatenating Vcf Files
Answer: Ti Tv ratio and their usefulness in exome sequencing
Answer: Ti Tv ratio and their usefulness in exome sequencing
Answer: How do you generate TMM normalized counts using EdgeR?
Answer: How do you generate TMM normalized counts using EdgeR?
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Commentator to GenoMax 142k
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Recent Replies
Comment: Super ehancers by Oburah • 0
python2.7 ROSE_main.py -g HG38 -i /home/hesborn/Desktop/Data/S3vS2-2.gff -r /home/hesborn/Downloads/possorted_bam.bam.bai -o Hezz -s 12500 …
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…
Comment: GATK Structural Variants Pipeline - Steps by Bioinformatics_begginner ▴ 20
Thank you for the response, I mean those tools aren't all the steps from fasta to vcf. Would be key understanding the aligner, reference us…
Comment: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from by GenoMax 142k
Please accept the answer (green check mark) to provide closure to this thread.
Answer: GATK Structural Variants Pipeline - Steps by Pierre Lindenbaum 161k
> A structural variation pipeline for short-read sequencing https://github.com/broadinstitute/gatk-sv
Comment: GATK Structural Variants Pipeline - Steps by DGTool ▴ 20
If it is just the tools that they used which you are looking for, the first link in the overview section of that page leads to the followin…
Comment: GO analysis: p-value range by Matthias Zepper 4.6k
It is just a warning that you add a new scale to a ggplot2 plot, that already has an existing one, which will get replaced. Nothing to worr…
Comment: GO analysis: p-value range by marco.barr ▴ 130
If you write me the code you used I can help you more
Comment: GO analysis: p-value range by sooni ▴ 20
When I run the code, the following message appears: Scale for y is already present. Adding another scale for y, which will replace…
Comment: Why most genes have high padj values by mnx0723 • 0
In the case of other samples, the total number of genes is at least 3,000 more than that one, but it seems to be a relatively small number.…
Comment: How to hide label in layout file of MCscan (python version) by jinyi • 0
Command line is as follows: python -m jcvi.graphics.synteny Cs.Cm.i1.blocks Cs_Cm.bed layout2.txt
Comment: Add stats to the plot by marco.barr ▴ 130
Thank you, it seems to be clearer. Your Condition already has two factorial levels. You can replace these names in groups 1 and 2. da…
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