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515 results • Page 2 of 11
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7
votes
11
replies
3.2k
views
Tool: Graphical User Interface for creating an automated RNA-Sequencing Pipeline via Kallisto and DESeq2
DESeq2 kallisto RNA-Seq
updated 11 months ago by 44k • written 5.4 years ago by ▴ 60
17
votes
11
replies
11k
views
6 follow
Tool: Pyfaidx: Efficient, "Pythonic" Random Access To Fasta Files Using Samtools-Compatible Indexing
fasta python samtools
updated 11 months ago by 44k • written 10.3 years ago by 10k
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 44k • written 6.3 years ago by ▴ 150
3
votes
10
replies
1.7k
views
Tool: Quick & dirty DNA coordinates in any mac app
sequence alignment
updated 11 months ago by 44k • written 6.2 years ago by ▴ 180
23
votes
10
replies
12k
views
Tool: ggtree: phylogenetic tree visualization and annotation
ggtree phylogeny visualization
updated 11 months ago by 44k • written 7.9 years ago by ★ 2.6k
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 44k • written 3.6 years ago by 8.6k
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 44k • written 5.8 years ago by ▴ 300
14
votes
10
replies
7.9k
views
Tool: ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization
ReactomePA R Visualization Pathway Bioconductor
updated 11 months ago by 44k • written 7.9 years ago by ★ 2.6k
17
votes
9
replies
6.1k
views
Tool: Pathomx: Metabolic Pathway Visualisation And Analysis
python pathway-visualization
updated 10 months ago by 44k • written 11.1 years ago by ▴ 180
3
votes
9
replies
3.6k
views
Tool: Download all refseq/genbank bacterial genomes from NCBI
genome sequencing
updated 11 months ago by 44k • written 7.3 years ago by ▴ 10
7
votes
9
replies
4.1k
views
Tool: VCF-simplify: a VCF simplification tool.
VCF variants genome
updated 11 months ago by 44k • written 6.1 years ago by ★ 1.6k
19
votes
9
replies
6.1k
views
Tool: Rlsim, A Package For Simulating Rna-Seq Library Preparation With Parameter Estimation
simulation rna-seq pcr illumina
updated 11 months ago by 44k • written 11.1 years ago by ★ 1.7k
8
votes
9
replies
9.0k
views
Tool: Lofreq: A Fast And Sensitive Variant-Caller For Inferring Single-Nucleotide Variants From Ngs Data
snp next-gen somatic-variant
updated 10 months ago by 44k • written 11.6 years ago by ★ 2.5k
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
34
votes
9
replies
11k
views
7 follow
Tool: Bwa-Meth: Align And Tabulate Bs-Seq Reads
methylation
updated 10 months ago by 44k • written 10.3 years ago by 24k
17
votes
9
replies
17k
views
6 follow
Tool: ggrepel: repel overlapping text labels in ggplot2
R visualization
updated 11 months ago by 44k • written 8.4 years ago by ★ 2.3k
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 44k • written 7.8 years ago by 8.3k
4
votes
9
replies
2.7k
views
Tool: CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.3 years ago by • 0
15
votes
9
replies
3.4k
views
Tool: FlexiDot: highly customizable, ambiguity-aware dotplots
dotplot visualization sequence-analysis
updated 11 months ago by 44k • written 6.0 years ago by ▴ 230
6
votes
8
replies
4.9k
views
Tool: Read-based phasing with WhatsHap
phasing
updated 11 months ago by 44k • written 7.4 years ago by ▴ 100
3
votes
8
replies
744
views
Tool: Generate unit-tested, ready-to-run pipelines using natural language prompting
NGS pipeline genomics cloud AI
updated 3 months ago by 44k • written 3 months ago by ▴ 50
22
votes
8
replies
6.6k
views
Tool: BioTuring Browser: Making single-cell sequencing data in published studies really accessible!
scRNA-Seq single-cell
updated 11 months ago by 44k • written 5.6 years ago by ▴ 580
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 44k • written 4.8 years ago by ★ 3.6k
2
votes
8
replies
3.7k
views
Tool: Mirnakey - A Software Pipeline For The Analysis Of Microrna Deep Sequencing Data
mirna
updated 11 months ago by 44k • written 11.8 years ago by 100k
3
votes
8
replies
6.3k
views
Tool: MFEprimer-2.0: A Fast Thermodynamics-Based Program For Checking Pcr Primer Specificity
primer pcr
updated 10 months ago by 44k • written 12.0 years ago by ▴ 170
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 44k • written 6.5 years ago by 161k
13
votes
8
replies
4.3k
views
Tool: MSigDB for Multiple Organisms in a Tidy Data Format
msigdb pathways R gsea
updated 11 months ago by 44k • written 6.1 years ago by 13k
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 44k • written 7.7 years ago by 5.3k
12
votes
7
replies
3.2k
views
Tool: Chromozoom: The Genome Browser That Lets You Fly!
genome-browser browser
updated 10 months ago by 44k • written 11.2 years ago by 100k
28
votes
7
replies
11k
views
Tool: Quast Is A Convenient Tool For Assembly Evaluation
assembly quality
updated 11 months ago by 44k • written 11.2 years ago by ★ 1.3k
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 44k • 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 44k • written 3.6 years ago by ★ 2.0k
7
votes
7
replies
4.7k
views
Tool: Variant Annotation, Analysis and Search Tool - VAAST2
VAAST2 VAAST
updated 10 months ago by 44k • written 10.1 years ago by 12k
3
votes
7
replies
1.4k
views
Tool: New method for protein secondary structure prediction
protein secondary-structure
updated 11 months ago by 44k • written 4.7 years ago by ▴ 180
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 44k • written 11.0 years ago by ▴ 40
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 11 months ago by 44k • written 7.2 years ago by ★ 2.5k
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 44k • written 6.1 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
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 11 months ago by 44k • written 7.0 years ago by ★ 2.5k
2
votes
7
replies
2.7k
views
Tool: metaflagstat.py - painless bam/sam read flag counting
samtools bam
updated 10 months ago by 44k • written 9.7 years ago by 13k
13
votes
7
replies
9.8k
views
Tool: Command-Line Software For Bigwig Data
bigwig
updated 11 months ago by 44k • written 10.6 years ago by ▴ 90
4
votes
7
replies
1.4k
views
Tool: Elloreas, a new genome assembler
Assembly next-gen
updated 11 months ago by 44k • written 3.9 years ago by ★ 1.2k
6
votes
6
replies
4.8k
views
Tool: Reading/ Writing FASTA files in Java
FASTA Java
updated 10 months ago by 44k • written 9.4 years ago by • 0
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 44k • written 10.7 years ago by ★ 5.3k
13
votes
6
replies
4.9k
views
Tool: GAWN - Genome Annotation Without Nightmares
genome-annotation
updated 11 months ago by 44k • written 6.8 years ago by 11k
27
votes
6
replies
16k
views
Tool: Bioawk - Fasta, Fastq, Sam, Bed, Gff Aware Awk Programming
awk
updated 10 months ago by 44k • written 11.9 years ago by 100k
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 44k • written 5.1 years ago by ▴ 80
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 44k • written 7.6 years ago by ▴ 80
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 44k • written 3.3 years ago by • 0
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
515 results • Page 2 of 11
Recent Votes
GO analysis: Different results EnrichGO vs ShinyGO
Comment: NGS forensics: how to know if data is fabricated
T2T-CHM13 "complete" human genome gff/gtf annotation file
Answer: T2T-CHM13 "complete" human genome gff/gtf annotation file
Comment: Problem in getting geo file through GEOQUERY
Answer: Problem in getting geo file through GEOQUERY
Comment: SnpEff and Snpsift
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Recent Replies
Comment: Functional enrichment analysis for unique gene IDs by Pegasus ▴ 100
Thanks for your answer, but as far as I know, gProfiler2 does not support bacteria. Could you please suggest alternative websites or softwa…
Comment: Create a new bed file with all pairwise combinations between two other bed files by J ▴ 10
Hi Alex, I'm sorry if I wasn't initially clear! The question hasn't changed; I had written in this post that I wanted all pairwise combinat…
Comment: BiomartException: Query ERROR for existing dataset in BioMart by Nyksubuz ▴ 20
Could share some examples for gene_ids?
Comment: Problem in getting geo file through GEOQUERY by anasjamshed ▴ 120
yeah but i am unable to find the link of GPL6244.soft.gz
Comment: Problem in getting geo file through GEOQUERY by ATpoint 82k
> Can you send me ftp link so I can download that soft file manually? Please find this link on your own by browsing the respective GEO ent…
Comment: Problem in getting geo file through GEOQUERY by anasjamshed ▴ 120
Thanks . I have downloaded all other files but just have problem in Error in downloadFile(myurl, destfile, mode = mode, quiet = TRUE)…
Answer: Problem in getting geo file through GEOQUERY by ATpoint 82k
Code runs for me and finishes in seconds. Maybe some poor internet connection on your end. Just set the timeout to 9999999 and retry. If th…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c by ezz3 • 0
Thanks. I was wondering if that is the case but was having some issues understanding the transanno code which is written in rust and I don…
Answer: Multi-ploid data in ANGSD and NGSadmix by andersdetermig ▴ 20
1 ) I would not expect the haploid individuals to always cluster together but the model assumptions are violated. First of all the diploid…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c by Pierre Lindenbaum 161k
"Are you using correct reference?" may be your reference is not using the same chrM. see https://www.biostars.org/p/199796/#199803
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument by shpak.max ▴ 50
Could you please elaborate on what you mean by passing -L or -V, i.e. what would the appropriate argument be for -L with UnifiedGenotyper f…
Answer: Add stats to the plot by Ghada • 0
It works. I have added this code my_comparisons=list(c("HRSV", "HRSV_RBV")) plot + stat_compare_means(method = "wilcox.test",…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument by LChart 3.9k
I believe UnifiedGenotyper is a locus walker that sets `emitEmptySites() = False`. As such you will not see entries for positions that have…
Comment: Problem in getting geo file through GEOQUERY by anasjamshed ▴ 120
Basically this is my code: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # # pkgs <- rowna…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument by shpak.max ▴ 50
If that were the case, I would expect there not to be any uncalled sites in the vcf, yet there are a large number of sites with "." placeho…
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