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670 results • Page 1 of 14
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2
votes
0
replies
44
views
Tool: Efficient querying of genomic reference databases with gget
ensembl
5 hours ago by Laura ▴ 20
1
vote
4
replies
162
views
Tool: Quick Command to Filter Bam Files
bed awk
1 day ago by Sasha • 0
2
votes
0
replies
101
views
Tool: OakVar: genomic variant analysis tool
genomics variant bioinformatics
4 days ago by Ryangguk Kim ▴ 80
26
votes
4
replies
12k
views
Tool: Plotting GSEA output in R
javaGSEA GSEA RNA-Seq plot Tool
updated 4 days ago by • 0 • written 5.8 years ago by ▴ 820
25
votes
19
replies
5.9k
views
10 follow
Tool: pathfindR - Enrichment Analysis using Active Subnetworks
enrichment pathway active subnetwork R Tool
updated 12 days ago by ▴ 10 • written 4.2 years ago by ★ 1.2k
1
vote
1
reply
211
views
Tool: Roakvar: do genomic variant analyses with R
oakvar genomics roakvar variant analysis
updated 14 days ago by 20k • written 14 days ago by ▴ 80
16
votes
3
replies
9.4k
views
Tool: Vcflib Documentation
vcf Tool
updated 24 days ago by • 0 • written 9.2 years ago by ★ 2.3k
38
votes
21
replies
14k
views
8 follow
Tool: pybam - 100% python BAM reader
python bam pysam htspython Tool
updated 4 weeks ago by • 0 • written 6.1 years ago by 13k
71
votes
14
replies
9.5k
views
10 follow
Tool: karyoploteR: uncircle your genomes
R Tool dataviz karyoploteR NGS
updated 4 weeks ago by • 0 • written 5.0 years ago by ★ 3.3k
0
votes
0
replies
89
views
Tool: Announcing the Papilloma Virus Episteme (PaVE) 2.0 Release
genomics HPV 3D
5 weeks ago by karlynn.noble ▴ 60
0
votes
0
replies
93
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
6 weeks ago by bigmawen ▴ 430
9
votes
7
replies
556
views
Tool: miniDBG - a Jupyter notebook for teaching De Bruijn Graph assembly
python deBruijnGraph de_bruijn_graph assembly teaching
4 weeks ago by Michael Dondrup 51k
2
votes
0
replies
167
views
Tool: Introducing ElasticBLAST – Run bigger BLAST searches faster on the Cloud
Tool NCBI BLAST ElasticBLAST
9 weeks ago by PeterC_NCBI ▴ 20
1
vote
1
reply
203
views
Tool: New VCF Header (schema) Parser---Please Break!!!
VCF header
updated 10 weeks ago by ★ 2.6k • written 10 weeks ago by ▴ 190
215
votes
36
replies
125k
views
27 follow
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
genome coordinates conversion liftover ensembl Tool
updated 11 weeks ago by ▴ 170 • written 9.2 years ago by 19k
5
votes
2
replies
1.8k
views
Tool: eLabFTW: a free and open source electronic lab notebook
software open-source free php Tool
3 months ago by Nico ▴ 190
1
vote
1
reply
2.9k
views
Tool: mirDIP 4.1 - integrative database of human microRNA target predictions
microRNA miRNA tool interactome targets Tool
updated 3 months ago by • 0 • written 4.0 years ago by ▴ 50
9
votes
20
replies
6.9k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
Tool software
3 months ago by vytarasov ▴ 160
2
votes
6
replies
2.1k
views
Tool: microbiomeMarker: microbiome biomarker analysis in R
microbiome lefse Tool stamp
updated 3 months ago by ▴ 540 • written 23 months ago by ▴ 30
5
votes
8
replies
4.0k
views
6 follow
Tool: Converting MUMmer snps file to a real VCF file
mummer SNP Tool conversion VCF
updated 3 months ago by • 0 • written 2.8 years ago by ★ 3.5k
5
votes
3
replies
501
views
Tool: Make a Sequence Logo in your browser by using native Javascript.
javascript sequence browser logo
4 months ago by Paul A. Gagniuc ▴ 40
0
votes
0
replies
148
views
Tool: Local sequence alignment made visual in your browser
javascript browser sequence alignment local
3 months ago by Paul A. Gagniuc ▴ 40
15
votes
11
replies
6.3k
views
Tool: Arriba: Fast and accurate gene fusion detection from RNA-Seq data
RNA-Seq cancer variant calling gene fusion Tool
4 months ago by uhrigs ▴ 150
0
votes
0
replies
154
views
Tool: AIQC - open source framework making deep learning accessible for researchers.
statistics machine multi-omic learning ai
4 months ago by syntax ▴ 60
28
votes
17
replies
3.2k
views
7 follow
Tool: PCAtools: everything Principal Components Analysis
pca eigenvector R bioconductor Tool
updated 4 months ago by • 0 • written 3.3 years ago by 81k
13
votes
7
replies
3.3k
views
Tool: I-PV: a CIRCOS module for interactive protein sequence visualization
circos interactive sequence javascript Tool
5 months ago by Ibrahim Tanyalcin ★ 1.2k
0
votes
1
reply
260
views
Tool: Molecular Dynamics analysis tools [desmond Schrodinger]
dynamics schrodinger desmond mdanalysis molecular
updated 6 months ago by 115k • written 6 months ago by • 0
0
votes
0
replies
193
views
Tool: SBGNview published online with Bioinformatics
Pathview BioConductor SBNGview visualization pathway
6 months ago by bigmawen ▴ 430
9
votes
5
replies
1.1k
views
Tool: Genozip: A new compression tool for FASTQ, BAM, VCF and more
bam vcf fastq compression
5 months ago by Divon ▴ 180
0
votes
0
replies
178
views
Tool: Proteome-pI 2.0 - Proteome Isoelectric Point Database
isoelectric_point protein pKa database proteomics
6 months ago by Lukasz Kozlowski • 0
4
votes
13
replies
1.4k
views
Tool: SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
Pathview SBGN pathway analysis visualization Tool
updated 7 months ago by • 0 • written 15 months ago by ▴ 430
1
vote
1
reply
418
views
Tool: Cell Type Prediction - covering 45 immune cell types
citeseq scRNA singlecell
updated 7 months ago by ▴ 40 • written 9 months ago by ▴ 580
3
votes
5
replies
1.3k
views
Tool: Extend 3' UTR of a GTF file
RNA-Seq annotation GTF python Tool
updated 7 months ago by • 0 • written 20 months ago by ▴ 620
10
votes
1
reply
700
views
Tool: fastp 0.23.0 released, runs 2x faster, and generates reproducible outputs.
FASTQ
updated 7 months ago by 115k • written 7 months ago by ★ 2.4k
1
vote
0
replies
233
views
Tool: A pairwise genome alignment pipeline using LAST and Nextflow
genome LAST Nextflow dotplot alignment
8 months ago by Charles Plessy ★ 2.8k
0
votes
0
replies
248
views
Tool: NGS-Barcode-Count
DEL NGS CRISPRseq
8 months ago by coffeyrt • 0
0
votes
0
replies
384
views
Tool: Utilising QIIME 2 pipeline: a current and future golden standard platform to analyze Amplicon-Seq data
Bioinformatics NGS Sequencing BI
8 months ago by Novogene ▴ 160
4
votes
0
replies
299
views
Tool: Annoyed by contig name inconsistencies (eg chr22 vs 22)? A solution
contigs bam vcf reference compression
8 months ago by Divon ▴ 180
0
votes
0
replies
280
views
Tool: Genotype Imputation Workflow
gwas imputation.
8 months ago by nhaus ▴ 200
1
vote
0
replies
217
views
Tool: shell script to search txt in academic figures
search_txt_in_image.sh
8 months ago by Zhilong Jia ★ 2.1k
0
votes
0
replies
492
views
Tool: Still Not Use QIIME2 for Amplicon Analysis? You’re OUT!
NGS analysis BI Bioinformatics Sequencing
8 months ago by Novogene ▴ 160
1
vote
2
replies
501
views
Tool: krust: a k-mer counter in Rust using the rust-bio and rayon crates
Rust kmer-counting fasta kmer
updated 8 months ago by 93k • written 8 months ago by ▴ 10
0
votes
1
reply
508
views
Tool: BioFileConverter - an app for Mac users to convert .xdna and .dna files into genbank .gb files and more
xdna file gb dna genbank
8 months ago by vytarasov ▴ 160
3
votes
3
replies
620
views
Tool: brename: safely batch renaming files/directories via regular expression
batch renaming
updated 8 months ago by 36k • written 8 months ago by 7.1k
0
votes
0
replies
363
views
Tool: Handy online tool for genomic analysis and data visualization - Part II
NGS analysis BI Bioinformatics Sequencing
updated 9 months ago by 20k • written 9 months ago by ▴ 160
1
vote
0
replies
246
views
Tool: Looking for feedback on epigenetics R package - enhancer detection and visualization
epigenetics chromatin enhancers atac chip
9 months ago by Alex ▴ 20
0
votes
0
replies
258
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
9 months ago by Emilio Marmol ▴ 150
50
votes
16
replies
12k
views
12 follow
Tool: Omictools: A didactic directory for omic data analysis (NGS, microarray, PCR, MS, NMR)
pcr Tool software ngs
updated 8 months ago by 36k • written 8.7 years ago by ▴ 450
1
vote
0
replies
278
views
Tool: Omics Playground: visualization and analysis of transcriptomics and proteomics data
proteomics RNA RNA-seq scRNA-seq omics data
10 months ago by bigomics.team ▴ 90
2
votes
2
replies
487
views
Tool: miRAnno—network-based functional microRNA annotation
pathways miRNA annotation microRNA
10 months ago by tomastokar ▴ 50
670 results • Page 1 of 14
Recent Votes
C: PI_HAT and Z-values for relationships (PLINK IBD calculation)
Efficient querying of genomic reference databases with gget
Integrating VDJ sequencing data with Seurat
Efficient querying of genomic reference databases with gget
Comment: how to fetch intron coordinates from transcriptome.gtf file ? is there any dir
A: Regression using genotype on expression of genes
A: How to use ALLPATH-LG assembler
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Recent Replies
Answer: enrichr by Laura ▴ 20
Use it through [gget enrichr][1] for super easy use! [1]: https://github.com/pachterlab/gget
Comment: DESeq2 use of factors for colData by swbarnes2 12k
I believe it will try to make a linear correlation between the logs of the counts and your numerical colData. But it's hard to know withou…
Comment: Difference in total gene counts between samples by swbarnes2 12k
I think it's glaringly obvious that library size is driving your first PC. I would not be at all confident that the typical techniques wil…
Answer: Retrieving ensembl protein length with biomart by Laura ▴ 20
*[gget][1] seq* will return the nucleotide (option "gene") or amino acid (option "transcript") sequence and sequence length for any Ensembl…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam by Pierre Lindenbaum 145k
`$1`: https://www.gnu.org/software/gawk/manual/gawk.html#Fields `/^@/`: https://www.gnu.org/software/gawk/manual/gawk.html#Regexp-Usage `…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam by I0110 ▴ 120
What is the "$1 ~ /^@/'" part for? Thanks!
Answer: fastq.gz download error by GenoMax 115k
This dataset appears to have been released just a few days back (20th May) so it may not be fully ready to download from ENA. $ curl …
Comment: fastq.gz download error by nishimalhotra2612 ▴ 10
I m downloading it directly from ENA database Generated fastq files:FTP And the operating system is windows 11 It's not the error but …
Comment: fastq.gz download error by lieven.sterck 13k
you'll need to provide some more (crucial) information here: how are you downloading it? (program? OS?) , what is the error you get? ... th…
Comment: snakemake r script by nishimalhotra2612 ▴ 10
thanks i will modify script and will install the needed package
Comment: snakemake r script by nishimalhotra2612 ▴ 10
thank you so much
Comment: Third Quartile (Q3) for RNAseq data by Leo • 0
I read that it is a common approach to use ConsensusClusterPlus. I am trying to figure out, are TCGA data_mrna_seq_v2_rsem.txt data already…
Comment: how to fetch intron coordinates from transcriptome.gtf file ? is there any dir by ATpoint 61k
Indeed, good catch!
Comment: how to fetch intron coordinates from transcriptome.gtf file ? is there any dir by rpolicastro 8.2k
If you want the exact intron ranges you would need to modify the above but by looking per transcript. Doing it per gene would give you regi…
Comment: PCA plot interpretation after accounting for batch effects with SVA by rpolicastro 8.2k
There doesn't appear to be an appreciable separation between the two conditions for most of your samples. Instead of immediately going to S…
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