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515 results • Page 1 of 11
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2
votes
0
replies
188
views
Tool: Sequence alignment on split read event such as inversion, duplication and complex nested events.
minimap alignment NGMLR
2 days ago by micah ▴ 30
4
votes
5
replies
4.4k
views
Tool: GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly Structural-Variation Variant-Calling
updated 4 days ago by ▴ 520 • written 7.2 years ago by ★ 2.9k
1
vote
3
replies
297
views
Tool: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes Decimal offtopic Degrees python
updated 4 days ago by 44k • written 6 days ago by ▴ 30
1
vote
1
reply
205
views
Tool: Collect dispersed executable files and run them by using bingo.
bingo
updated 4 days ago by 44k • written 5 days ago by ▴ 10
1
vote
1
reply
254
views
Tool: Converting Nebula Genomics Data to 23andMe Format
23andMe Nebula
updated 14 days ago by 54k • written 14 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
212
views
Tool: pySEACR
Peak-Calling CUT-and-RUN
5 weeks ago by Adam ▴ 30
2
votes
3
replies
512
views
Tool: DEGap - an online tool for Differential Gene Expression analysis
degap
6 weeks ago by Anastasia ▴ 10
2
votes
1
reply
376
views
Tool: TGSFilter, An ultra-fast and efficient tool for long reads filtering and trimming
genome-assembly filtering reads trimming
updated 8 weeks ago by • 0 • written 8 weeks ago by ▴ 190
0
votes
0
replies
242
views
Tool: MicrobiomePhylo: A Comprehensive Platform for Advanced Microbiome Amplicon Sequencing Data Analysis and Visualization
microbiome analysis data 16S
8 weeks ago by camillatafuro • 0
85
votes
46
replies
9.3k
views
15 follow
Tool: ChatGPT optimized for bioinformatics questions
gpt
updated 9 weeks ago by 4.2k • written 11 months ago by ▴ 850
5
votes
2
replies
2.5k
views
Tool: Coovar: Co-Occurring Variant Analyzer
snp variant-annotation
updated 10 weeks ago by 142k • written 11.6 years ago by ★ 3.0k
1
vote
4
replies
439
views
Tool: A c library for reading and writing sequences in fasta and fastq format.
seqio
10 weeks ago by dwpeng ▴ 10
1
vote
0
replies
255
views
Tool: HFKReads, an ultra-fast and efficient tool for high frequency kmer sequencing reads extraction
kmer organelle metagenomic assembly
12 weeks ago by Huiyang ▴ 190
0
votes
0
replies
295
views
Tool: Microbiome Analysis: Comprehensive 16S Meta-barcoding Analysis in R with Phyloseq - On Sale Now!
R microbiome 16S phyloseq analysis
11 weeks ago by camillatafuro • 0
0
votes
0
replies
180
views
Tool: Annotating the epitope-specificity of TCRs with bioinformatics
Annotation TCR Epitope-specificity
3 months ago by tim • 0
10
votes
12
replies
1.9k
views
Tool: PanDepth, an ultra-fast and efficient genomic tool for coverage calculation
bam paf depth cram coverage
3 months ago by Huiyang ▴ 190
1
vote
0
replies
276
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
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
0
replies
241
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
227
views
Tool: BIRCH3.90 - BioLegato, Apple Silicon, Updates
genomics sequence transcriptomics
3 months ago by brian.fristensky ▴ 460
0
votes
0
replies
218
views
Tool: Get `BPCells` with Bioconductor workflow
single cell BPCells
3 months ago by Yun • 0
1
vote
3
replies
690
views
Tool: retroSeeker: discovering a large set of retrotransposons in humans and any species
Mobile-element Evolution Retrotransposon
4 months ago by lsp03yjh ▴ 860
1
vote
0
replies
289
views
Tool: tinybio in OpenAI App Store
gpt
4 months ago by Sasha ▴ 850
0
votes
0
replies
873
views
Tool: What do you think about Tfinder? a tool to find individual motifs in DNA sequence. Help us ameliorate
Motifs Transcription-factor
updated 5 months ago by 44k • written 5 months ago by • 0
0
votes
2
replies
418
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 5 months ago by 44k • written 5 months ago by ★ 1.2k
1
vote
0
replies
253
views
Tool: De Novo assembler (in C, supports MPI parallelism) available for experimenting with
de-novo trie olc
updated 5 months ago by 44k • written 5 months ago by ▴ 10
4
votes
0
replies
477
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
6 months ago by Hugo ▴ 380
0
votes
0
replies
550
views
Tool: deepBreaks: a machine learning tool for identifying and prioritizing genotype-phenotype associations
python genetics
updated 6 months ago by 44k • written 6 months ago by • 0
1
vote
1
reply
409
views
Tool: Coremine Medical Introduction - connect - discover - share | explore and visualize associations
drug-target drug gene
updated 6 months ago by 44k • written 6 months ago by ▴ 20
0
votes
0
replies
247
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
284
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
325
views
Tool: Introducing SpectraView - a tool to transform your literature reviews!
gene protein drug-discovery
updated 7 months ago by 44k • written 7 months ago by • 0
4
votes
0
replies
399
views
Tool: MyBrain-Seq: A Pipeline for MiRNA-Seq Data Analysis in Neuropsychiatric Disorders
mybrain-seq miRNA-seq pipeline neuropsychiatry docker
7 months ago by dannyzimm ▴ 50
12
votes
4
replies
1.1k
views
Tool: BBTools 39.03 released!
BBTools BBMap
7 months ago by Brian Bushnell 20k
2
votes
2
replies
605
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
302
views
Tool: MTMCSKAT package for GWAS with efficient resampling, parallelization
SKAT MTMC-SKAT
updated 8 months ago by 44k • written 8 months ago by ▴ 100
11
votes
2
replies
785
views
Tool: Pipeline Generator
gpt
updated 9 months ago by 4.2k • written 9 months ago by ▴ 850
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
3
votes
1
reply
842
views
Tool: pyGenomeViz - A genome visualization python package for comparative genomics
genome comparative-genomics python microbial-genomics visualization
updated 4 months ago by ▴ 90 • written 9 months ago by ▴ 150
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
0
votes
2
replies
7.9k
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
604
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
3.6k
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 10.6 years ago by • 0
3
votes
2
replies
801
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
514
views
Tool: tinybio added sources & chat history - (ChatGPT optimized for bioinformatics questions)
gpt
updated 8 weeks ago by • 0 • written 10 months ago by ▴ 850
7
votes
4
replies
2.9k
views
Tool: TreeView3 - An update to java TreeView
TreeView3 java
updated 9 months ago by ▴ 10 • written 5.9 years ago by ▴ 180
0
votes
0
replies
379
views
Tool: Unleashing the Power of Custom NGS Software for Cutting-Edge Research
DNAseq pipeline bisulfiteSeq RNAseq
updated 11 months ago by 13k • written 11 months ago by 11k
5
votes
3
replies
875
views
Tool: Experiment Generator
gpt
updated 11 months ago by 4.2k • written 11 months ago by ▴ 850
515 results • Page 1 of 11
Recent Votes
Answer: Question about samtools view flags (paired reads vs. properly paired reads)
Answer: Functional enrichment analysis for unique gene IDs
Comment: Super ehancers
Comment: Why does assigning genes with biomart give me different values than using a tran
Comment: Multiplexing for pooled CRISPR screen sequencing
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
Answer: Differential Expression with limma: Contrast and Design Matrix, combinatorial ap
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Recent Replies
Comment: Question about samtools view flags (paired reads vs. properly paired reads) by Pierre Lindenbaum 161k
> Thanks. What determines what constitutes a good distance? I think tools like BWA use the median distance for each chunk of processed d…
Comment: Where are the illumina adapters on Trimmomatic take from? by bioinfo ▴ 150
Thank you for the explanation. Is it more appropriate then to use the sequence from the illumina documentation or the one from the github?
Comment: Question about samtools view flags (paired reads vs. properly paired reads) by mrk • 0
Thanks. What determines what constitutes a good distance? I have some targeted panel data and looking at flagstat, almost all reads are pai…
Comment: Where are the illumina adapters on Trimmomatic take from? by GenoMax 142k
Illumina indexed adapters share a core sequence at the beginning which is what is indicated in your link. Trimming programs will remove seq…
Comment: Allele count of 2 for homoplasmic MT variants in VCF by Ram 44k
Please stop using `bioinformatics` as a tag unless your post is about the field of bioinformatics itself.
Comment: Multiplexing for pooled CRISPR screen sequencing by GenoMax 142k
> If we switch to pair-end sequencing with dual-index barcode You can use dual-indexing with single end reads. You don't need to do paired…
Comment: Super ehancers by jared.andrews07 ★ 17k
That is not valid GFF format, so that is probably going to be problematic. See the [GFF spec](https://github.com/The-Sequence-Ontology/Spec…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors) by finch • 0
Hey! I had this issue and I think I can help- could you take a screenshot of the .txt file opened in the notepad?
Answer: Is it possible to run CibersortX with a very small number of samples? by finch • 0
Hi! I had a very similar issue and it's likely not at all related to your number of samples but to the format of your mixture file! Ciberso…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w by Ram 44k
You cannot *convert* a VCF to a FASTA as they have vastly different information content. Please explain your process - what exactly do you …
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o by Shukai • 0
Thank you Ram for the comments! Noted for future posts.
Comment: Where to find old version of GATK best practice by Zhenyu Zhang ★ 1.2k
I am looking for diagrams, and step-by-step instructions of how to build my pipelines. I think the github is only helpful if you are a wdl…
Comment: Where to find old version of GATK best practice by Zhenyu Zhang ★ 1.2k
oh, this is helpful. Thanks.
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o by Ram 44k
1. You can edit your post and add relevant details. There is no need to add separate comments with relevant details especially when it's no…
Answer: Functional enrichment analysis for unique gene IDs by geneontologyhelp ▴ 410
If you are looking at producing GO annotations, we currently only recommend InterProScan, and basically only for novel organisms or where t…
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