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734 results • Page 1 of 15
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1
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208
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Tool: Converting Nebula Genomics Data to 23andMe Format
23andMe Nebula
updated 2 days ago by 54k • written 3 days ago by • 0
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
2
votes
0
replies
206
views
Tool: pySEACR
Peak-Calling CUT-and-RUN
28 days ago by Adam ▴ 30
2
votes
3
replies
499
views
Tool: DEGap - an online tool for Differential Gene Expression analysis
degap
4 weeks ago by Anastasia ▴ 10
2
votes
1
reply
366
views
Tool: TGSFilter, An ultra-fast and efficient tool for long reads filtering and trimming
genome-assembly filtering reads trimming
updated 6 weeks ago by • 0 • written 6 weeks ago by ▴ 190
0
votes
0
replies
233
views
Tool: MicrobiomePhylo: A Comprehensive Platform for Advanced Microbiome Amplicon Sequencing Data Analysis and Visualization
microbiome analysis data 16S
6 weeks ago by camillatafuro • 0
83
votes
46
replies
9.1k
views
15 follow
Tool: ChatGPT optimized for bioinformatics questions
gpt
updated 8 weeks ago by 4.2k • written 11 months ago by ▴ 840
5
votes
2
replies
2.5k
views
Tool: Coovar: Co-Occurring Variant Analyzer
snp variant-annotation
updated 9 weeks ago by 142k • written 11.5 years ago by ★ 3.0k
1
vote
4
replies
424
views
Tool: A c library for reading and writing sequences in fasta and fastq format.
seqio
9 weeks ago by dwpeng • 0
1
vote
0
replies
248
views
Tool: HFKReads, an ultra-fast and efficient tool for high frequency kmer sequencing reads extraction
kmer organelle metagenomic assembly
10 weeks ago by Huiyang ▴ 190
0
votes
0
replies
285
views
Tool: Microbiome Analysis: Comprehensive 16S Meta-barcoding Analysis in R with Phyloseq - On Sale Now!
R microbiome 16S phyloseq analysis
9 weeks ago by camillatafuro • 0
0
votes
0
replies
172
views
Tool: Annotating the epitope-specificity of TCRs with bioinformatics
Annotation TCR Epitope-specificity
12 weeks ago by tim • 0
10
votes
12
replies
1.8k
views
Tool: PanDepth, an ultra-fast and efficient genomic tool for coverage calculation
bam paf depth cram coverage
12 weeks ago by Huiyang ▴ 190
1
vote
0
replies
262
views
Tool: gxf2bed: A high-performance GTF/GFF-to-BED converter written in Rust
convert gff gtf bed
3 months ago by alejandrogzi ▴ 120
3
votes
8
replies
727
views
Tool: Generate unit-tested, ready-to-run pipelines using natural language prompting
NGS pipeline genomics cloud AI
updated 3 months ago by 43k • written 3 months ago by ▴ 50
3
votes
0
replies
227
views
Tool: GW: fast genome browser and variant exploration tool
genome genomics variant-annotation genome-browser visualization
3 months ago by clealk ▴ 50
1
vote
0
replies
219
views
Tool: BIRCH3.90 - BioLegato, Apple Silicon, Updates
genomics sequence transcriptomics
3 months ago by brian.fristensky ▴ 460
0
votes
0
replies
212
views
Tool: Get `BPCells` with Bioconductor workflow
single cell BPCells
3 months ago by Yun • 0
1
vote
3
replies
669
views
Tool: retroSeeker: discovering a large set of retrotransposons in humans and any species
Mobile-element Evolution Retrotransposon
3 months ago by lsp03yjh ▴ 860
1
vote
0
replies
277
views
Tool: tinybio in OpenAI App Store
gpt
3 months ago by Sasha ▴ 840
0
votes
0
replies
866
views
Tool: What do you think about Tfinder? a tool to find individual motifs in DNA sequence. Help us ameliorate
Motifs Transcription-factor
updated 4 months ago by 43k • written 4 months ago by • 0
0
votes
2
replies
404
views
Tool: Dot_plot_like_in_BLAST, a standalone tool for making dot plots similar to what online BLAST makes
Megablast Blastn dot plot dotplot BLAST
updated 4 months ago by 43k • written 4 months ago by ★ 1.2k
1
vote
0
replies
247
views
Tool: De Novo assembler (in C, supports MPI parallelism) available for experimenting with
de-novo trie olc
updated 5 months ago by 43k • written 5 months ago by ▴ 10
4
votes
0
replies
469
views
Tool: NOEL: An extremely fast Non-Overlapping Exon Length calculator written in Rust
gene-annotation exon-length
5 months ago by alejandrogzi ▴ 120
9
votes
4
replies
2.3k
views
Tool: SEDA (SEquence DAtaset builder): a desktop tool for processing FASTA files containing DNA and protein sequences
fasta sequences java
5 months ago by Hugo ▴ 380
0
votes
0
replies
545
views
Tool: deepBreaks: a machine learning tool for identifying and prioritizing genotype-phenotype associations
python genetics
updated 6 months ago by 43k • written 6 months ago by • 0
1
vote
1
reply
402
views
Tool: Coremine Medical Introduction - connect - discover - share | explore and visualize associations
drug-target drug gene
updated 6 months ago by 43k • written 6 months ago by ▴ 20
0
votes
0
replies
243
views
Tool: massSight: A tool to combine LC-MS datasets
qc metabolomics omics R lc-ms
6 months ago by Chiraag • 0
0
votes
0
replies
280
views
Tool: Coremine Medical used in study to discover differentially expressed genes in multiple sclerosis
drugs drug-targets genes
6 months ago by Coremine Medical ▴ 20
0
votes
0
replies
321
views
Tool: Introducing SpectraView - a tool to transform your literature reviews!
gene protein drug-discovery
updated 6 months ago by 43k • written 6 months ago by • 0
4
votes
0
replies
381
views
Tool: MyBrain-Seq: A Pipeline for MiRNA-Seq Data Analysis in Neuropsychiatric Disorders
mybrain-seq miRNA-seq pipeline neuropsychiatry docker
6 months ago by dannyzimm ▴ 50
12
votes
4
replies
1.1k
views
Tool: BBTools 39.03 released!
BBTools BBMap
6 months ago by Brian Bushnell 20k
2
votes
2
replies
599
views
Tool: Python and R without installing apps
Resources
updated 8 months ago by ▴ 290 • written 8 months ago by ▴ 20
0
votes
0
replies
296
views
Tool: MTMCSKAT package for GWAS with efficient resampling, parallelization
SKAT MTMC-SKAT
updated 8 months ago by 43k • written 8 months ago by ▴ 100
11
votes
2
replies
778
views
Tool: Pipeline Generator
gpt
updated 8 months ago by 4.2k • written 8 months ago by ▴ 840
13
votes
6
replies
5.2k
views
Tool: csvtk - a cross-platform, efficient, practical and pretty CSV/TSV toolkit
CSV Golang TSV
8 months ago by shenwei356 8.5k
3
votes
1
reply
825
views
Tool: pyGenomeViz - A genome visualization python package for comparative genomics
genome comparative-genomics python microbial-genomics visualization
updated 3 months ago by ▴ 90 • written 9 months ago by ▴ 150
9
votes
9
replies
4.6k
views
Tool: pyCirclize - Circular visualization in Python
visualization circos matplotlib genome python
updated 9 months ago by • 0 • written 16 months ago by ▴ 150
0
votes
2
replies
7.8k
views
Tool: The script to install the required packages for gene expression analysis using DESeq2 for downstream analysis and visualization
R RNAseq installation DESeq2
9 months ago by Aditya naman • 0
1
vote
0
replies
592
views
Tool: Create realistic VCF genomic data in just a few lines of Python code
genomic linkage python vcf tool disequilibrium
9 months ago by Rémy ▴ 10
1
vote
2
replies
3.5k
views
Tool: How Study Aromatic-Aromatic Interactions And Amino-Aromatic Interactions Of Protein-Ligands Complexes In The Pdb.
pdb
updated 10 months ago by ▴ 370 • written 10.5 years ago by • 0
3
votes
2
replies
783
views
Tool: Launched: Genozip 15 with co-compression of BAM and FASTQ
BAM CRAM compression FASTQ
updated 10 months ago by ▴ 300 • written 10 months ago by ▴ 230
0
votes
1
reply
505
views
Tool: tinybio added sources & chat history - (ChatGPT optimized for bioinformatics questions)
gpt
updated 6 weeks ago by • 0 • written 10 months ago by ▴ 840
7
votes
4
replies
2.9k
views
Tool: TreeView3 - An update to java TreeView
TreeView3 java
updated 8 months ago by ▴ 10 • written 5.9 years ago by ▴ 180
0
votes
0
replies
374
views
Tool: Unleashing the Power of Custom NGS Software for Cutting-Edge Research
DNAseq pipeline bisulfiteSeq RNAseq
updated 10 months ago by 13k • written 10 months ago by 11k
5
votes
3
replies
857
views
Tool: Experiment Generator
gpt
updated 11 months ago by 4.2k • written 11 months ago by ▴ 840
0
votes
0
replies
500
views
Tool: Easy API For Running Bioinformatics Jobs Via Python In The Cloud
api execution
11 months ago by Sasha ▴ 840
0
votes
0
replies
481
views
Tool: Single-cell RNA-seq data analysis tool Cellenics®
single-cell RNA-seq scRNA-seq
updated 11 months ago by 43k • written 11 months ago by • 0
0
votes
1
reply
988
views
Tool: web app for user-friendly analysis of 16S rRNA gene meta-barcoding NGS data - bacterial microbiome
qiime2 16s microbiome ngs
updated 12 months ago by 43k • written 12 months ago by • 0
1
vote
2
replies
864
views
Tool: Tinybio Slackbot - a large language model slackbot for bioinformatics
qa
12 months ago by Sasha ▴ 840
734 results • Page 1 of 15
Recent Votes
How to use minimap2?
Comment: RNA seq analysis
Comment: Filtering Multi-sample VCF file for all except one Genotype
Truncated metadata file report from ENA Portal API
Comment: Truncated metadata file report from ENA Portal API
A: Download data from TCGA
A: Do I need to normalize level 3 TCGA data?
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Recent Replies
Comment: RNA seq analysis by prifa ▴ 10
it's raw data **fastq.gz**, so for example I have 4 different samples from different tissue, sample A with 3 replicates, samples B,C and D …
Answer: Filtering Multi-sample VCF file for all except one Genotype by Pierre Lindenbaum 161k
> The goal is to remove all the variants which are unique to the KWSBambina sample. using jvarkit vcffilterjdk https://jvarkit.readthedo…
Comment: Too many unpaired forward reads found by Trimmomatic by SilhouetteQ • 0
The first example used the adapter file NexteraPE-PE.fa, but it generated more than 50% unpaired data...... The content of NexteraPE-PE.fa…
Comment: Filtering Multi-sample VCF file for all except one Genotype by schmince • 0
Ok so I definitely didn't understand at first what my goal was. The goal is to remove all the variants which are unique to the KWSBambina…
Comment: Question about methylation location by dthorbur ★ 1.9k
What data do you have? Generally, you start with sequencing data, which you need to clean and then map to a reference genome. Then dependin…
Comment: Too many unpaired forward reads found by Trimmomatic by GenoMax 142k
> when I didn't provide the adapter file Still see the file here `ILLUMINACLIP:./NexteraPE-PE.fa:2:30:10 `, unless that is an empty file.
Comment: Too many unpaired forward reads found by Trimmomatic by SilhouetteQ • 0
Interestingly, when I didn't provide the adapter file, the number of unpaired forward reads was significantly reduced: TrimmomaticPE…
Comment: Alignment of samples with spike-in by GenoMax 142k
> but then if you only allow to map uniquely mapped reads, you are losing spike-in information, How so? Spike-in's are generally unique s…
Comment: Truncated metadata file report from ENA Portal API by GenoMax 142k
While there is no timeout by default on the `get` operation, you may want to set a higher value and see if that helps, since there is a lar…
Comment: Truncated metadata file report from ENA Portal API by Giulia • 0
The " missing is because of a copy-paste error in the post.. I know wget but my tool is entirely in python. I really don't understand why i…
Comment: UMI-Tools knee-method has great influence on the results of white list by Assa Yeroslaviz ★ 1.8k
and if I use the command as such: ``` umi_tools extract --extract-method=regex --error-correct-cell \ --bc-pattern2='(?P…
Comment: UMI-Tools knee-method has great influence on the results of white list by i.sudbery 19k
No, UMI-tools won't work this out automatically, you'll need to either switch read1 and read2 or use the new `--read2-only` which is curren…
Comment: Correlation Analysis by manaswwm ▴ 510
If your *gene_corr* data frame contains one gene instead of all genes, then the correlation would be per gene. If your *gene_corr* data fra…
Comment: UMI-Tools knee-method has great influence on the results of white list by Assa Yeroslaviz ★ 1.8k
I think I might know my problem. The barcodes are in this case on read2 and not on read1. Does umi-tools recognise it automatically, or do …
Comment: Microbial Signal Transduction Database by zx8754 11k
Did you try https://mib-jouline-db.asc.ohio-state.edu/#introduction ? >The database can also be accessed via the API. The same API points …
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