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635 results • Page 1 of 13
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4
votes
1
reply
2.8k
views
Tool: Clustering of short peptide sequences
peptide clustering phage display Tool
updated 3 days ago by • 0 • written 5.5 years ago by ▴ 390
0
votes
0
replies
56
views
Tool: FileSlide.io - Annotating and distributing sequencing data from the web
data-distribution data-annotation data-sharing
6 days ago by Simon • 0
2
votes
1
reply
134
views
Tool: Bioinformatics Programming Package
Package Tools Bioinformatics
updated 13 days ago by 32k • written 13 days ago by ▴ 10
46
votes
26
replies
5.8k
views
9 follow
Tool: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
sra sequence-read-archive fastq download Tool
19 days ago by Phil Ewels ▴ 620
3
votes
1
reply
186
views
Tool: VCF2PopTree: build a phylogenetic tree from a VCF file
VCF2Phylogenetictree
updated 20 days ago by ▴ 190 • written 24 days ago by ▴ 40
5
votes
4
replies
2.0k
views
Tool: Converting MUMmer snps file to a real VCF file
VCF mummer conversion SNP Tool
updated 24 days ago by • 0 • written 20 months ago by ★ 3.4k
2
votes
0
replies
86
views
Tool: New Tuberculosis in 3D Interactive Viewer
tuberculosis viewer 3D
25 days ago by karlynn.noble ▴ 60
13
votes
10
replies
4.5k
views
Tool: Arriba: Fast and accurate gene fusion detection from RNA-Seq data
RNA-Seq cancer variant calling gene fusion Tool
29 days ago by uhrigs ▴ 130
2
votes
0
replies
169
views
Tool: New location tracking tool for SARS-CoV-2 variant surveillance
tool data variant covid-19 sars-cov-2 Tool
4 weeks ago by ehaag ▴ 20
9
votes
6
replies
628
views
Tool: DiffBind 3.0: Extensive updates in Bioconductor 3.12
ChIP-Seq DiffBind ATAC-seq chipseq diffbind Tool
updated 4 weeks ago by • 0 • written 5 months ago by ★ 1.0k
7
votes
5
replies
1.6k
views
Tool: AGAT - Another Gff/Gtf Analysis Toolkit
annotation gff gtf toolkit Tool
5 weeks ago by Juke34 ★ 5.4k
3
votes
12
replies
568
views
Tool: SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
Pathview SBGN pathway analysis visualization Tool
5 weeks ago by bigmawen ▴ 400
18
votes
39
replies
1.6k
views
Tool: CBioInfCpp.h as a C++ lib containing some functions for bioinformatics
Tool C++ tool c++
5 weeks ago by chernouhov sergey ▴ 50
6
votes
12
replies
3.7k
views
Tool: New Mac program for molecular biologists
software Tool
5 weeks ago by vytarasov ▴ 110
1
vote
5
replies
972
views
Tool: microbiomeMarker: microbiome biomarker analysis in R
microbiome lefse Tool stamp
updated 6 weeks ago by ▴ 40 • written 10 months ago by ▴ 20
3
votes
1
reply
393
views
Tool: Introducing Gallia: a Scala library for data manipulation
scala spark etl json vcf Tool
6 weeks ago by cros.anthony ▴ 30
5
votes
5
replies
270
views
Tool: ClusterProfiler A software for functional enrichment of differentially expressed genes
rna-seq tool Software Tool clusterProfiler
4 days ago by guoxuantong ▴ 120
0
votes
0
replies
289
views
Tool: I made QMplot: a python library and tools of generating high-quality manhattan and Q-Q plots for GWAS data
GWAS visualization genome Python Manhattan Plot Tool
7 weeks ago by huangshujia9 • 0
33
votes
7
replies
25k
views
Tool: Tools to merge overlapping paired-end reads
overlapping Assembly ngs fastq Tool
updated 8 weeks ago by • 0 • written 4.4 years ago by ★ 1.1k
13
votes
2
replies
948
views
Tool: EnhancedVolcano becomes a pseudo-EnhancedMA
enhancedvolcano enhancedMA Tool
updated 8 weeks ago by ▴ 120 • written 7 months ago by 72k
4
votes
0
replies
280
views
Tool: rBCS & pyBCS: open-source packages to support interactive visualizations of single-cell data
scrna-seq single-cell rna-seq Tool
8 weeks ago by Jennifer Pham ▴ 420
0
votes
0
replies
174
views
Tool: MultiLink Analysis: Brain Network Comparison via Sparse Connectivity Analysis
brain connectome networks neuroscience tool Tool
9 weeks ago by alex.crimi • 0
1
vote
0
replies
146
views
Tool: BiOkeanos - the largest(*) biomedical database catalogue and discovery tool
data database catalogue Tool
9 weeks ago by ellimilial ▴ 20
0
votes
0
replies
177
views
Tool: Analyze & Visualize Nephele Microbiome Results Using MicrobiomeDB
microbiome sequence Tool
9 weeks ago by karlynn.noble ▴ 60
22
votes
20
replies
2.9k
views
Tool: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
sam bam markduplicates sort bqsr Tool
9 weeks ago by Charlotte.Herzeel ▴ 150
7
votes
10
replies
435
views
Tool: SamReadViewer - A small utility to visualise read alignment directly from sam format without reference.
sam viewer read Tool
updated 10 weeks ago by 12k • written 6 months ago by ★ 5.4k
0
votes
0
replies
178
views
Tool: Cytoscape Network analysis
software error Tool
10 weeks ago by subhasisdehury • 0
6
votes
6
replies
2.6k
views
Tool: chromoMap- R package for Interactive visualization and Annotation of chromosomes or regions of any living organism.
R genome annotation visualization Tool
updated 11 weeks ago by • 0 • written 2.0 years ago by ▴ 60
0
votes
1
reply
189
views
Tool: GMAP gff wrong direction of transcripts?
RNA-Seq rna-seq alignment Assembly assembly Tool
12 weeks ago by maria • 0
0
votes
3
replies
208
views
Tool: Script: Getting information about SRX experiment ID from NCBI database
RNA-Seq rna-seq next-gen Blog Tool
12 weeks ago by jayeshkumarsundaram • 0
0
votes
6
replies
188
views
Tool: Script: Downloading fastq files from ENA database
rna-seq RNA-Seq sequencing next-gen Tool
12 weeks ago by jayeshkumarsundaram • 0
0
votes
1
reply
210
views
Tool: CHIP-Seq data mapping using Bowtie2
ChIP-Seq Mapping Tool
updated 12 weeks ago by ▴ 110 • written 12 weeks ago by • 0
11
votes
2
replies
4.5k
views
Tool: fastp (the ultra-fast all-in-one FASTQ preprocessing tool) v0.18.0 released, 2X faster, with many new features.
fastp Tool QC filtering
updated 3 months ago by ▴ 20 • written 2.8 years ago by ★ 2.1k
198
votes
30
replies
112k
views
22 follow
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
genome coordinates conversion liftover ensembl Tool
updated 3 months ago by • 0 • written 8.1 years ago by 18k
2
votes
3
replies
457
views
Tool: Extend 3' UTR of a GTF file
RNA-Seq annotation GTF python Tool
3 months ago by Shred ▴ 300
4
votes
2
replies
421
views
Tool: Alternate the wild type and mutant of SARS-CoV-2 N501Y
SNP Tool
3 months ago by Jiyao Wang ▴ 70
24
votes
26
replies
1.3k
views
Tool: ClinCNV: CNV detection from short reads
cnv cna variant calling Tool
4 months ago by German.M.Demidov ★ 2.0k
73
votes
79
replies
17k
views
17 follow
Tool: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
compression bbmap clumpify pigz storage Tool
updated 4 months ago by • 0 • written 4.4 years ago by 17k
34
votes
30
replies
572
views
6 follow
Tool: BioFlows - Container-enabled Bioinformatics pipeline engine
pipeline bioinformatics RNA-Seq workflow next-gen Tool
updated 26 days ago by 32k • written 4 months ago by ▴ 80
341
votes
80
replies
123k
views
32 follow
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
tools parallel next-gen ngs Tool
4 months ago by ole.tange ★ 4.0k
0
votes
0
replies
361
views
Tool: Annotation tools (prokaryotes): prokka vs eggnog
eggnog prokka annotations assembly HMM Tool
4 months ago by willnotburn ▴ 40
1
vote
3
replies
222
views
Tool: Filtering BAM files efficiently
BAM SAM alignment genome Tool
4 months ago by ddeemer • 0
14
votes
13
replies
2.1k
views
Tool: trackplot: Fast and minimal dependency standalone R script to generate IGV style locus tracks from bigWig files
ChIP-Seq bigwigs igv R visualization Tool
updated 4 months ago by ▴ 20 • written 4 months ago by ★ 3.0k
9
votes
3
replies
989
views
Tool: SEDA (SEquence DAtaset builder): a desktop tool for processing FASTA files containing DNA and protein sequences
sequences fasta java bioinformatics Tool
4 months ago by Hugo ▴ 340
2
votes
1
reply
389
views
Tool: Alternate wild type and mutant of SNPs in 3D
SNP Jupyter Notebook 3D viewer iCn3D Tool
4 months ago by Jiyao Wang ▴ 70
3
votes
0
replies
271
views
Tool: ChromSCape - A R/Shiny application to analyze single-cell epigenomics data
ChIP-Seq scChIP-seq scATAC-seq single-cell R Tool
4 months ago by pacome.pr ▴ 100
2
votes
0
replies
219
views
Tool: driveR - Prioritizing Cancer Driver Genes Using Genomics Data
driver R cancer driver gene Tool
4 months ago by egeulgen ★ 1.1k
1
vote
0
replies
188
views
Tool: VTAM: Validation and Taxonomic Assignation of Metabarcoding Data
metabarcoding python amplicon vsearch Tool
5 months ago by aitor.gonzalez ▴ 20
1
vote
2
replies
379
views
Tool: Graphia: A platform for the graph-based visualisation and analysis of complex data
networks transcriptomics high dimensional data Tool
5 months ago by Tom Freeman ▴ 10
3
votes
0
replies
294
views
Tool: Trimviz, a lightweight QC tool to assess impact of read-trimming and aligner soft-clipping
QC trimming clipping fastq alignment Tool
5 months ago by stuart archer ▴ 70
635 results • Page 1 of 13
Recent Votes
Installing perl modules on a conda environment produce changes out of the environment?
Answer: Installing perl modules on a conda environment produce changes out of the enviro
Answer: Installing perl modules on a conda environment produce changes out of the enviro
DESeq2 Pre-filtering and Subsetting
How To Analyze Imputed Gwas Data
How To Analyze Imputed Gwas Data
Comment: RNAseq data analysis of pooled data
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Recent Replies
Comment: Parsing df with pandas and some conditions by stevejonn • 0
The simplest solution would be to read the "[Unnamed: 0][1]" column as the index. So, what you have to do is to specify an index_col=[0] ar…
Answer: Installing perl modules on a conda environment produce changes out of the enviro by Philipp Bayer 6.9k
You can check using `which perl` - it should give you the perl that's located within your conda environment. In this case, it should instal…
Comment: single tumor vs multiple normal sample differential gene expression (RNA-Seq ) a by sumitguptabt ▴ 10
Dear, please help me, I am new in this field. Please tell me if it is the right way or needs some correction.
Comment: RNAseq by Kevin Blighe 72k
Hi, can you please choose a more informative question title? Also, can you take a look at how I use `gffread`, here: https://www.biostars.…
Comment: Up-to-date GWAS Power Calculator and GWAS power comparison by moxu ▴ 480
Hi Kevin, Thanks for the reply. I had checked out CaTS before posting above. However, I am not sure if CaTS does what I want to do. Suppo…
Comment: Arlequin problem (different loci number among different genotypes) by wangh920 • 0
For sure, The reason why this happen is because SNP calling generate a couple of biallelic SNP, such as GC, GT or GCT, GCG. These allelic…
Answer: Make New Orig.ident in seurat object or by fracarb8 ▴ 140
You can use `strsplit` to extract the first entry before the `_` metadata <- seurat_object@meta.data metadata$orig.ident <- …
Comment: How to solve the problem when I get error message "column 1 is not a genotype ob by Bornali • 0
Hi Devon Ryan. I am trying to add genotype object to my SNP data set. I am unable to use the codes described in the subsequent comment as m…
Comment: Duplicated Gene Symbol names after geneID conversion by asumani ▴ 70
opss, didn't notice that thread. many thanks!
Answer: Duplicated Gene Symbol names after geneID conversion by GenoMax 99k
See: https://www.biostars.org/p/352492/#352535
Comment: Can't count features with featurecount by avelarbio46 ▴ 10
After using these options, I got decreased aligment in general than with "-F GTF -s 0 -p -T 8 -a ". I have not tried with -M and -O on 1 or…
Comment: How to merge two GTFs which share some common features by GenoMax 99k
See the answers and discussion in: https://www.biostars.org/p/9465577/
Comment: single tumor vs multiple normal sample differential gene expression (RNA-Seq ) a by sumitguptabt ▴ 10
Dear @atpoint Thank you so much for your help, I can not describe my happiness. I run your script and got the output as you see in the att…
Comment: How to run SPAdes assembler with bam files? by GenoMax 99k
Sorted files compress better so the size being smaller is not a particular surprise. Have you checked to see that you are getting reads at …
Comment: How to run SPAdes assembler with bam files? by marongiu.luigi ▴ 560
Thank you. Actually I am getting an unmapped.bam file of 132 Mb, a sorted version of 34 Mb (shouldn't they be the same weight) and fastq of…
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