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515 results • Page 2 of 11
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21
votes
11
replies
11k
views
Tool: Segemehl: A Fast One-Stop-Shop Mapping Tool
mapping next-gen
updated 10 months ago by 44k • written 11.7 years ago by 11k
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 5.7 years ago by ▴ 580
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
12
votes
6
replies
3.5k
views
Tool: Variant annotation and filtration server ALAPY Genome Explorer (AGx)
vcf variant-annotation variant-interpretation
updated 11 months ago by 44k • written 7.0 years ago by ★ 2.8k
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
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
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 44k • written 10.7 years ago by 22k
2
votes
6
replies
2.1k
views
Tool: Primer design shiny app
SNP sequencing
updated 11 months ago by 44k • written 7.6 years ago by ▴ 10
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
2
votes
6
replies
5.2k
views
Tool: Variantannotation Package (Bioconductor)
snp variant-annotation
updated 10 months ago by 44k • written 11.8 years ago by 20k
515 results • Page 2 of 11
Recent Votes
Construction of circos plot from WGS data
Answer: Different SNP at the at a position in vcf file compared to REF and ALT allele.
Answer: Different SNP at the at a position in vcf file compared to REF and ALT allele.
Different SNP at the at a position in vcf file compared to REF and ALT allele.
Comment: downloading chemical database from ChEMBL
Seurat-Merging and integrate
voom mean-variance plot has set of genes where variance increases with expression level
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Recent Replies
Answer: from CRAM to fastq by Pierre Lindenbaum 161k
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.
Comment: downloading chemical database from ChEMBL by GenoMax 142k
Activities with `cucurbitacin A`: https://www.ebi.ac.uk/chembl/web_components/explore/activities/STATE_ID:RHxG8uDfrtbmiyaY55ic-w%3D%3D `cu…
Comment: KEGG analysis in R by letizia.ottaviani • 0
Hello, I have a problem to do the analysis in R. I want to kindly ask you: How did you perform KEGG pathway enrichment analysis in R for…
Comment: downloading chemical database from ChEMBL by s • 0
Thank you for your reply. I am still struggling with the first step, namely "select a compound" . can you be more specific with this step? …
Comment: No output when converting transcript IDs to gene symbols by ATpoint 82k
Honestly, why the overhead with biomart? Get a GTF file that matches your annotations, and just do a left join with your transcript IDs, it…
Answer: vg autoindex seems stuck after a week of running by Jouni Sirén ▴ 370
GCSA construction is fragile. It can use effectively unlimited amounts of time, memory, and disk space if the graph is too complex. That's …
Comment: Blastn, need help to increase speed by Dunois ★ 2.5k
What databases are you using that are creating such large index files?
Answer: Kraken2 Custom Database non-deterministic results by colindaven 6.4k
You're using 2 different databases, so results are obviously different. This has nothing to do with deterministic or stochastic behaviour. …
Answer: How to get 2 seurat objects into a DEseq by ultraanfibio ▴ 30
Its probably best practice to read all samples into the same seurat object, then do the clustering and asign the cell type labels. Anyways …
Comment: How do we do quantification using stringtie merge option for all the merged samp by ATpoint 82k
I ask the same I always ask when people use stringtie for human data. Do you really need a transcript assembly or do you just want gene cou…
Comment: Mapping difference with BWA by ATpoint 82k
Cannot be answered without more details. At least add accessions and commands.
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