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733 results • Page 1 of 15
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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
203
views
Tool: pySEACR
Peak-Calling CUT-and-RUN
24 days ago by Adam ▴ 30
2
votes
3
replies
491
views
Tool: DEGap - an online tool for Differential Gene Expression analysis
degap
26 days ago by Anastasia ▴ 10
2
votes
1
reply
362
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
231
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
9.0k
views
15 follow
Tool: ChatGPT optimized for bioinformatics questions
gpt
updated 7 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 8 weeks ago by 142k • written 11.5 years ago by ★ 3.0k
1
vote
4
replies
419
views
Tool: A c library for reading and writing sequences in fasta and fastq format.
seqio
8 weeks ago by dwpeng • 0
1
vote
0
replies
246
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
282
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
171
views
Tool: Annotating the epitope-specificity of TCRs with bioinformatics
Annotation TCR Epitope-specificity
11 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
11 weeks ago by Huiyang ▴ 190
1
vote
0
replies
257
views
Tool: gxf2bed: A high-performance GTF/GFF-to-BED converter written in Rust
convert gff gtf bed
12 weeks ago by alejandrogzi ▴ 120
3
votes
8
replies
724
views
Tool: Generate unit-tested, ready-to-run pipelines using natural language prompting
NGS pipeline genomics cloud AI
updated 12 weeks ago by 43k • written 3 months ago by ▴ 50
3
votes
0
replies
224
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
217
views
Tool: BIRCH3.90 - BioLegato, Apple Silicon, Updates
genomics sequence transcriptomics
3 months ago by brian.fristensky ▴ 460
0
votes
0
replies
209
views
Tool: Get `BPCells` with Bioconductor workflow
single cell BPCells
3 months ago by Yun • 0
1
vote
3
replies
662
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
272
views
Tool: tinybio in OpenAI App Store
gpt
3 months ago by Sasha ▴ 840
0
votes
0
replies
863
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
401
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
246
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
466
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
400
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
5 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
376
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
597
views
Tool: Python and R without installing apps
Resources
updated 7 months ago by ▴ 290 • written 8 months ago by ▴ 20
0
votes
0
replies
294
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
773
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
818
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
8 months ago by Aditya naman • 0
1
vote
0
replies
580
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
782
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
504
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 5.8 years ago by ▴ 180
0
votes
0
replies
372
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
856
views
Tool: Experiment Generator
gpt
updated 10 months ago by 4.2k • written 10 months ago by ▴ 840
0
votes
0
replies
499
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
476
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
987
views
Tool: web app for user-friendly analysis of 16S rRNA gene meta-barcoding NGS data - bacterial microbiome
qiime2 16s microbiome ngs
updated 11 months ago by 43k • written 12 months ago by • 0
1
vote
2
replies
863
views
Tool: Tinybio Slackbot - a large language model slackbot for bioinformatics
qa
12 months ago by Sasha ▴ 840
0
votes
0
replies
458
views
Tool: shinyCircos-V2.0: leveraging the creation of Circos plot with enhanced usability and advanced features
shinyCircos visualization Circular Circos genome
12 months ago by Andrewoods ▴ 110
733 results • Page 1 of 15
Recent Votes
Answer: ERROR When Using Ensembl Plants Biomart Wget API
Answer: Should I remove these cells? (scRNA 10x 5')
Answer: STRING-DB API can't find my protein but I can find it when I go to the STRING-DB
Answer: STRING-DB API can't find my protein but I can find it when I go to the STRING-DB
A: Fold change - a final explanation
Answer: sc/snRNASeq using cell ranger parameters
mitochondria in single nuclear RNAseq
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Recent Replies
Comment: ERROR When Using Ensembl Plants Biomart Wget API by Dora ▴ 10
Thank you very much, that works perfectly :) ! Maybe someone needs to use a plant dataset as an example (instead of human dataset ) in the …
Comment: Truncated Bam Error by guanghao • 0
I also have this problem, but it doesn't work even I remove the Xms32g. The result bam is still malformed.
Answer: DMRcate ranges liftover hg19 to hg38 by aaron.stevens • 0
Hey, I believe they are mapped to hg19 and this is potentially a bigger problem than people realise, I nearly made this mistake and I would…
Comment: STRING-DB API can't find my protein but I can find it when I go to the STRING-DB by brandon • 0
This worked beautifully using 'requests.get()' in python, thank you so much!
Answer: STRING-DB API can't find my protein but I can find it when I go to the STRING-DB by Pierre Lindenbaum 161k
first get the main ID in stringdb: $ wget -qO - "https://string-db.org/api/tsv-no-header/get_string_ids?identifiers=RPS4Y1&species=960…
Comment: Help with DGEList function by marco.barr ▴ 90
Are you sure you've loaded the library properly? Have you checked if edgeR is ticked in the list of installed packages? Double-check it. If…
Comment: Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so t by mropri ▴ 150
Hi, I just wanted to update that IEGscore and PCNAscore were linearly dependent (or linear combinations of each other). I tested this using…
Comment: TaxID mapping file by Lada ▴ 30
if I understood correctly, I might need fle `prot.accession2taxid.gz` file? According to the [documentation][1] in column 2 is Accession.ve…
Answer: install package by Pine ▴ 10
To follow on Mathew's reply, one way might be to try and see if you can download and install the package tarball locally: 1. Get the packag…
Comment: agilent human all exon sureselct v7 bed file by MiladAD ▴ 10
God bless you man.
Answer: install package by Mathew ▴ 50
Hi, This is what happens when I run some code to diagnose the issue. First, I wanted to see what version of R was required for the package…
Comment: TaxID mapping file by Lada ▴ 30
thank you, I'll look at these files/documents. .
Answer: LD-prune variants while maintaining a list of SNPs by Jautis ▴ 540
I was given a solution by a colleague -- it seems a little hacky, but worked really well! > one way to get this to work is to use --clu…
Answer: Association study using SNP data by drajangirija • 0
Hi Matthew, Thank you very much for your inputs. I am working with Neogen genotyping data, which includes GC values less than 0.15.
Comment: Downloading full alignments from Pfam by bef1 • 0
I tried contacting Pfam, they replied that indeed there is an issue on their side with the full alignments, which should be repaired in the…
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