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738 results • Page 3 of 15
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16
votes
3
replies
11k
views
Tool: Vcflib Documentation
vcf
updated 11 months ago by 44k • written 11.2 years ago by ★ 2.4k
38
votes
21
replies
19k
views
8 follow
Tool: pybam - 100% python BAM reader
python htspython bam pysam
updated 11 months ago by 44k • written 8.1 years ago by 13k
76
votes
14
replies
13k
views
10 follow
Tool: karyoploteR: uncircle your genomes
karyoploteR Rdataviz NGS
updated 11 months ago by 44k • written 7.0 years ago by ★ 3.4k
0
votes
0
replies
433
views
Tool: Announcing the Papilloma Virus Episteme (PaVE) 2.0 Release
genomics HPV 3D
2.1 years ago by karlynn.noble ▴ 60
0
votes
0
replies
405
views
Tool: Nature Communications: New AI tool for in-depth cleaning of a wide range of noise in single-cell RNA-Seq data
denoise scRNA-Seq AutoClass AI
2.1 years ago by bigmawen ▴ 430
9
votes
7
replies
1.7k
views
Tool: miniDBG - a Jupyter notebook for teaching De Bruijn Graph assembly
python deBruijnGraph de_bruijn_graph assembly teaching
2.1 years ago by Michael 54k
2
votes
0
replies
597
views
Tool: Introducing ElasticBLAST – Run bigger BLAST searches faster on the Cloud
ElasticBLAST BLAST NCBI
updated 11 months ago by 44k • written 2.2 years ago by ▴ 410
1
vote
1
reply
615
views
Tool: New VCF Header (schema) Parser---Please Break!!!
VCF header
updated 2.2 years ago by ★ 2.9k • written 2.2 years ago by ▴ 250
231
votes
38
replies
147k
views
29 follow
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl genome-coordinates liftover
updated 11 months ago by 44k • written 11.2 years ago by 20k
5
votes
2
replies
2.4k
views
Tool: eLabFTW: a free and open source electronic lab notebook
elabftw free-open-source-software php
updated 11 months ago by 44k • written 4.7 years ago by ▴ 190
1
vote
1
reply
3.7k
views
Tool: mirDIP 4.1 - integrative database of human microRNA target predictions
interactome miRNA targets microRNA
updated 11 months ago by 44k • written 6.0 years ago by ▴ 50
2
votes
6
replies
3.5k
views
Tool: microbiomeMarker: microbiome biomarker analysis in R
stamp microbiome lefse
updated 11 months ago by 44k • written 3.9 years ago by ▴ 30
5
votes
8
replies
7.1k
views
6 follow
Tool: Converting MUMmer snps file to a real VCF file
VCF mummer SNP
updated 11 months ago by 44k • written 4.8 years ago by ★ 3.6k
4
votes
3
replies
1.3k
views
Tool: Make a Sequence Logo in your browser by using native Javascript.
javascript sequence browser logo
2.3 years ago by Paul A. Gagniuc ▴ 30
0
votes
0
replies
472
views
Tool: Local sequence alignment made visual in your browser
javascript browser sequence alignment local
2.3 years ago by Paul A. Gagniuc ▴ 30
15
votes
11
replies
8.3k
views
Tool: Arriba: Fast and accurate gene fusion detection from RNA-Seq data
variant-calling RNA-Seq cancer gene-fusion
updated 11 months ago by 44k • written 6.3 years ago by ▴ 150
0
votes
0
replies
484
views
Tool: AIQC - open source framework making deep learning accessible for researchers.
statistics machine multi-omic learning ai
2.4 years ago by Kermit ▴ 90
28
votes
17
replies
5.1k
views
7 follow
Tool: PCAtools: everything Principal Components Analysis
eigenvector pca bioconductor R
updated 11 months ago by 44k • written 5.3 years ago by 88k
13
votes
7
replies
4.2k
views
Tool: I-PV: a CIRCOS module for interactive protein sequence visualization
interactive javascript circos sequence
updated 21 months ago by 44k • written 8.6 years ago by ★ 1.2k
0
votes
1
reply
691
views
Tool: Molecular Dynamics analysis tools [desmond Schrodinger]
dynamics schrodinger desmond mdanalysis molecular
updated 2.5 years ago by 142k • written 2.5 years ago by • 0
0
votes
0
replies
524
views
Tool: SBGNview published online with Bioinformatics
Pathview BioConductor SBNGview visualization pathway
2.5 years ago by bigmawen ▴ 430
10
votes
5
replies
2.5k
views
Tool: Genozip: A new compression tool for FASTQ, BAM, VCF and more
bam vcf fastq compression
11 months ago by Divon ▴ 230
0
votes
0
replies
446
views
Tool: Proteome-pI 2.0 - Proteome Isoelectric Point Database
isoelectric_point protein pKa database proteomics
2.6 years ago by Lukasz Kozlowski • 0
4
votes
13
replies
2.8k
views
Tool: SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
pathway-analysis visualization Pathview SBGN
updated 11 months ago by 44k • written 3.2 years ago by ▴ 430
1
vote
1
reply
925
views
Tool: Cell Type Prediction - covering 45 immune cell types
citeseq scRNA singlecell
updated 2.6 years ago by ▴ 50 • written 2.8 years ago by ▴ 580
3
votes
5
replies
2.8k
views
Tool: Extend 3' UTR of a GTF file
annotation python RNA-Seq GTF
updated 11 months ago by 44k • written 3.7 years ago by ★ 1.4k
10
votes
1
reply
1.5k
views
Tool: fastp 0.23.0 released, runs 2x faster, and generates reproducible outputs.
FASTQ
updated 2.6 years ago by 142k • written 2.6 years ago by ★ 2.5k
1
vote
0
replies
605
views
Tool: A pairwise genome alignment pipeline using LAST and Nextflow
genome LAST Nextflow dotplot alignment
2.7 years ago by Charles Plessy ★ 2.9k
0
votes
0
replies
593
views
Tool: NGS-Barcode-Count
DEL NGS CRISPRseq
2.7 years ago by coffeyrt • 0
0
votes
0
replies
1.3k
views
Tool: Utilising QIIME 2 pipeline: a current and future golden standard platform to analyze Amplicon-Seq data
NGS Sequencing
updated 15 months ago by 44k • written 2.7 years ago by ▴ 420
4
votes
0
replies
740
views
Tool: Annoyed by contig name inconsistencies (eg chr22 vs 22)? A solution
contigs bam vcf reference compression
2.7 years ago by Divon ▴ 230
0
votes
0
replies
693
views
Tool: Genotype Imputation Workflow
gwas imputation.
2.7 years ago by nhaus ▴ 360
1
vote
0
replies
500
views
Tool: shell script to search txt in academic figures
search_txt_in_image.sh
2.7 years ago by Zhilong Jia ★ 2.2k
0
votes
0
replies
1.1k
views
Tool: Still Not Use QIIME2 for Amplicon Analysis? You’re OUT!
NGS Sequencing
updated 15 months ago by 44k • written 2.7 years ago by ▴ 420
1
vote
2
replies
993
views
Tool: krust: a k-mer counter in Rust using the rust-bio and rayon crates
Rust kmer-counting fasta kmer
updated 2.7 years ago by 100k • written 2.7 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Tool: BioFileConverter - an app for Mac users to convert .xdna and .dna files into genbank .gb files and more
dna genbank xdna
updated 14 months ago by 44k • written 2.7 years ago by ▴ 180
4
votes
3
replies
1.4k
views
Tool: brename: safely batch renaming files/directories via regular expression
batch renaming
updated 2.7 years ago by 44k • written 2.7 years ago by 8.5k
0
votes
0
replies
1.2k
views
Tool: Handy online tool for genomic analysis and data visualization - Part II
NGS Sequencing
updated 14 months ago by 44k • written 2.8 years ago by ▴ 420
1
vote
0
replies
523
views
Tool: Looking for feedback on epigenetics R package - enhancer detection and visualization
epigenetics chromatin enhancers atac chip
2.8 years ago by Alex ▴ 20
0
votes
0
replies
566
views
Tool: A framework to prioritize miRNA-driven post-transcriptional signals using exonic and intronic regions of RNAseq data
post-transcriptional miRNA intron exon RNAseq
2.8 years ago by Emilio Marmol ▴ 170
50
votes
16
replies
14k
views
12 follow
Tool: Omictools: A didactic directory for omic data analysis (NGS, microarray, PCR, MS, NMR)
pcr software ngs
updated 11 months ago by 44k • written 10.7 years ago by ▴ 450
1
vote
0
replies
584
views
Tool: Omics Playground: visualization and analysis of transcriptomics and proteomics data
proteomics RNA RNA-seq scRNA-seq omics data
2.8 years ago by bigomics.team ▴ 90
2
votes
2
replies
1.0k
views
Tool: miRAnno—network-based functional microRNA annotation
pathways miRNA annotation microRNA
2.8 years ago by tomastokar ▴ 50
21
votes
14
replies
9.6k
views
Tool: trackplot: Fast and minimal dependency standalone R script to generate IGV style locus tracks from bigWig files
visualization igv ChIP-Seq R bigwigs
updated 11 months ago by 44k • written 3.5 years ago by ★ 3.2k
1
vote
0
replies
2.0k
views
Tool: Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
biomart annotation Ensembl
2.8 years ago by Shred ★ 1.4k
1
vote
0
replies
559
views
Tool: BIRCH Bioinformatics System v3.80
alignment RNA-seq genome assembly sequence phylogeny
2.8 years ago by brian.fristensky ▴ 460
0
votes
0
replies
594
views
Tool: Manticore: a software to extract the intermixed regions of subgenomes in hybrid species
mapping hybrid subgenome genomics sequencing
2.9 years ago by Matteo Schiavinato ★ 3.6k
3
votes
1
reply
1.2k
views
Tool: all2vcf: a tool to convert non-standard variant outputs (mummer. bcftools isec) to VCF
mummer isec variant bcftools VCF
updated 19 months ago by • 0 • written 2.9 years ago by ★ 3.6k
0
votes
0
replies
1.0k
views
Tool: Handy online tool for genomic analysis and data visualization - Part I
NGS Sequencing
updated 14 months ago by 44k • written 2.9 years ago by ▴ 420
2
votes
0
replies
673
views
Tool: metaGEM: create your own genome scale metabolic models directly from metagenomes
metagenomics metagenome-assembled-genome genome-scale-metabolic-model metabolism
updated 2.9 years ago by 44k • written 2.9 years ago by ▴ 20
738 results • Page 3 of 15
Recent Votes
Answer: Log-transformation, coefficient of variation, standard error and mass-spectromet
Log-transformation, coefficient of variation, standard error and mass-spectrometry based proteomics
Log-transformation, coefficient of variation, standard error and mass-spectrometry based proteomics
Comment: Setting a threshold on gene expression for subsetting (scRNA-seq)
Comment: Difference between Genotype 0|1 and 1|0 in VCF file?
Answer: Difference between Genotype 0|1 and 1|0 in VCF file?
Answer: Difference between Genotype 0|1 and 1|0 in VCF file?
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Recent Replies
Answer: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by jared.andrews07 ★ 17k
Go back to your original counts matrix or input data and assign consistent IDs during its generation.
Answer: Facing problem with single cell rna seq annotation using singleR by jared.andrews07 ★ 17k
A few things. >(1)What did i do wrong here? SingleR will annotate each cell with whatever it's most similar to in the reference datas…
Comment: Harmony integration group.by.var parameter by jared.andrews07 ★ 17k
Couldn't tell you, I avoid Seurat like the plague.
Comment: What is the best practice of scRNA workflow for multiple patients and samples us by Picasa ▴ 640
Same. did you get any solution ?
Comment: Setting a threshold on gene expression for subsetting (scRNA-seq) by LauferVA 4.2k
Generally, I cannot advise this in the abstract. The thing is, depending on the treatment group and so forth, there are some transcripts th…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by Ram 44k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: Getting differential ChIP-seq peaks between conditions after calling consensus p by Alexandra • 0
Thank you for your response! Interesting paper.
Comment: How to scrape BioMart data from https://sorfs.ugent.be/ website by Pierre Lindenbaum 162k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: Harmony integration group.by.var parameter by Picasa ▴ 640
@jaredandrews07 If I integrate using Donor: ```R RunHarmony(seu_obj, group.by.vars = c("Donor_ID")) ``` Should I also normalize my data…
Comment: How to scrape BioMart data from https://sorfs.ugent.be/ website by QX • 0
thank you so much!
Comment: Attempt to set 'rownames' on an object with no dimensions by elbakri.fatimazahrae • 0
hello everyone, I got the same error for a function immuCellAI_new; result <- ImmuCellAI_new(countData = expr_data_log22, data_type =…
Comment: Merging multiple samples in Seurat by Picasa ▴ 640
did you split by sample or donor ?
Comment: Harmony integration group.by.var parameter by Picasa ▴ 640
For downstream analysis, after integration, my plan is to annotate each cluster/cell type and then perform a DGE analysis of KO versus WT f…
Comment: How to calculate cell type frequency between two groups in single cell data by Bastien Hervé 5.3k
That is correct
Comment: Setting a threshold on gene expression for subsetting (scRNA-seq) by ATpoint 82k
That depends on the data and the marker. Generally I would plot violins per cluster for the marker(s) and see whether one robustly overexpr…
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