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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
3 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 5 days ago by ▴ 520 • written 7.2 years ago by ★ 2.9k
1
vote
3
replies
304
views
Tool: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes Decimal offtopic Degrees python
updated 5 days ago by 44k • written 6 days ago by ▴ 30
1
vote
1
reply
207
views
Tool: Collect dispersed executable files and run them by using bingo.
bingo
updated 5 days ago by 44k • written 6 days ago by ▴ 10
1
vote
1
reply
257
views
Tool: Converting Nebula Genomics Data to 23andMe Format
23andMe Nebula
updated 14 days ago by 54k • written 15 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
213
views
Tool: pySEACR
Peak-Calling CUT-and-RUN
5 weeks ago by Adam ▴ 30
2
votes
3
replies
513
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
4 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
419
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
478
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
400
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
606
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
845
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
605
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
802
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
515
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
Comment: error when installing gistic2 using conda
Mean Length Of Fasta Sequences
C: Sequence length from Fasta
Sequence length from Fasta
vg autoindex seems stuck after a week of running
Answer: geom_bar issue in ggplot2 with xlim()
A: How Can I Get The Human Chromosome Centromere Position And Chromosome Length In
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Recent Replies
Answer: vg autoindex seems stuck after a week of running by Jouni Sirén ▴ 360
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: vg autoindex seems stuck after a week of running by ATpoint 82k
Is it even running? Use `top` or the Activity Monitor to check if there is activity in the job, or if it is sitting idle indicating corrupt…
Comment: Mapping difference with BWA by ATpoint 82k
Cannot be answered without more details. At least add accessions and commands.
Comment: vcf phasing by safeassli ▴ 10
Sprry but I'm not an expert in this field. I'm trying to learn Only 0/1, 1/0, and 1/1 genotypes should be phased, as these indicate the pr…
Comment: z-score of gene set by Hien • 0
I have a list of genes in some pathways, I want to see these pathways which are upregulated or downregulated in a total of gene expressions…
Comment: Splitting query fasta file for Diamond Blastp make the process faster? by kmat • 0
Thank you for your quick responce. Sorry for the lack of explanation. Here are some supplementary details regarding the parameters of Diam…
Answer: Splitting query fasta file for Diamond Blastp make the process faster? by Mensur Dlakic ★ 27k
There are several pieces of information we are missing here. Did you specify that all 96 threads be used? If so, are all of them being used…
Comment: BiomartException: Query ERROR for existing dataset in BioMart by Luqman • 0
Yes please see below: TraesCS2B02G372900 TraesCS2B02G375100 TraesCS2B02G374700 TraesCS2B02G382000
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?
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