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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
202
views
Tool: pySEACR
Peak-Calling CUT-and-RUN
22 days ago by Adam ▴ 30
2
votes
3
replies
489
views
Tool: DEGap - an online tool for Differential Gene Expression analysis
degap
25 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 5 weeks ago by • 0 • written 5 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
5 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
416
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
245
views
Tool: HFKReads, an ultra-fast and efficient tool for high frequency kmer sequencing reads extraction
kmer organelle metagenomic assembly
9 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
169
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
255
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
722
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 12 weeks ago by ▴ 50
3
votes
0
replies
223
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
862
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
244
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
465
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
544
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
397
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
242
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
279
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
319
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
375
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
595
views
Tool: Python and R without installing apps
Resources
updated 7 months ago by ▴ 290 • written 7 months ago by ▴ 20
0
votes
0
replies
294
views
Tool: MTMCSKAT package for GWAS with efficient resampling, parallelization
SKAT MTMC-SKAT
updated 7 months ago by 43k • written 7 months ago by ▴ 100
11
votes
2
replies
772
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
817
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 8 months ago by ▴ 150
9
votes
9
replies
4.6k
views
Tool: pyCirclize - Circular visualization in Python
visualization circos matplotlib genome python
updated 8 months ago by • 0 • written 16 months ago by ▴ 150
0
votes
2
replies
7.7k
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
579
views
Tool: Create realistic VCF genomic data in just a few lines of Python code
genomic linkage python vcf tool disequilibrium
8 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
371
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
854
views
Tool: Experiment Generator
gpt
updated 10 months ago by 4.2k • written 10 months ago by ▴ 840
0
votes
0
replies
497
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
985
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
862
views
Tool: Tinybio Slackbot - a large language model slackbot for bioinformatics
qa
11 months ago by Sasha ▴ 840
0
votes
0
replies
456
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: Design matrix Differential expression analysis
A: extract dendrogram cluster from pheatmap
extract dendrogram cluster from pheatmap
Answer: Searching for gene in multiple genomes
Comment: RNA velocity for smart-seq2 dataset
Answer: RNA velocity for smart-seq2 dataset
Answer: RNA velocity for smart-seq2 dataset
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Recent Replies
Comment: Design matrix Differential expression analysis by SHN ▴ 40
Thank you for your explanation. I am working on the cell lines and I am investigating the effect of the treatment on the expression level, …
Answer: Issues with Mixture file when using CIBERSORTx by vjanve • 0
I ran into same issue of "duplicated gene symbol(s)": 1: In CIBERSORTxFractions(sigmatrix = sigmatrix, mixture = mixture, : 22292 dup…
Comment: creating batch colum for batch correction by Expert ▴ 10
Thank you for your response. These samples were collected from the same patient at different time points(day 0, 8 and 18) and these are ind…
Comment: creating batch colum for batch correction by ATpoint 82k
Not sure I follow. Can you first of all describe which comparisons you want to make, pretending there was no batch effect at all. Write dow…
Comment: Pindel Segmentation Fault Error by Ruqaiya • 0
This the tool still problematic?
Comment: Segmentation error while using a tool by Ruqaiya • 0
Thank you for the advice, i'll keep that in mind.
Comment: Segmentation error while using a tool by Ruqaiya • 0
I am trying to reproduce some bioinformatics data from a research paper-[this paper][1] as i was asked to work on an MRSA bioinfo project, …
Answer: Segmentation error while using a tool by Mensur Dlakic ★ 27k
Most likely you didn't do anything wrong. Going by your previous post that you have only 8 GB of RAM, the most likely reason is the lack of…
Comment: Segmentation error while using a tool by Thanujay S • 0
Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why …
Comment: Extracting mutation status from MAF files - TCGA by Thanujay S • 0
Hey! Can you explain the question further? What have you tried?
Comment: Downloading older version of a tool by Ruqaiya • 0
I tried the 2nd option only. I got the files of older version from the author but that version isn't working on my WSL, it's showing Segmen…
Comment: filtering before dada2 by GenoMax 142k
> I encountered a significant decrease in the percentage of merged reads. You can check with `bbmerge.sh` from BBMap suite to see how many…
Comment: HCL database download by GenoMax 142k
Isn't the download link available above the plot: http://bis.zju.edu.cn/HCL/data/DGE/Adult-Transverse-Colon1_dge.txt.gz
Comment: fastq screen aligner no specified. by GenoMax 142k
You need to change this configuration file to point it to the location where the aligner executable can be found. So as an example followi…
Answer: Design matrix Differential expression analysis by Gordon Smyth ★ 7.1k
The expression levels do not change but the way that you have parametrized the expression levels does change. The two design matrices give…
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