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734 results • Page 3 of 15
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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
2.0 years ago by Michael 54k
2
votes
0
replies
593
views
Tool: Introducing ElasticBLAST – Run bigger BLAST searches faster on the Cloud
ElasticBLAST BLAST NCBI
updated 10 months ago by 43k • written 2.1 years ago by ▴ 410
1
vote
1
reply
608
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
146k
views
29 follow
Tool: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
ensembl genome-coordinates liftover
updated 10 months ago by 43k • 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 10 months ago by 43k • written 4.6 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 10 months ago by 43k • written 5.9 years ago by ▴ 50
2
votes
6
replies
3.4k
views
Tool: microbiomeMarker: microbiome biomarker analysis in R
stamp microbiome lefse
updated 10 months ago by 43k • written 3.9 years ago by ▴ 30
5
votes
8
replies
7.0k
views
6 follow
Tool: Converting MUMmer snps file to a real VCF file
VCF mummer SNP
updated 10 months ago by 43k • written 4.7 years ago by ★ 3.6k
4
votes
3
replies
1.2k
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
468
views
Tool: Local sequence alignment made visual in your browser
javascript browser sequence alignment local
2.2 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 10 months ago by 43k • written 6.2 years ago by ▴ 150
0
votes
0
replies
480
views
Tool: AIQC - open source framework making deep learning accessible for researchers.
statistics machine multi-omic learning ai
2.3 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 10 months ago by 43k • written 5.3 years ago by 87k
13
votes
7
replies
4.2k
views
Tool: I-PV: a CIRCOS module for interactive protein sequence visualization
interactive javascript circos sequence
updated 20 months ago by 43k • written 8.5 years ago by ★ 1.2k
0
votes
1
reply
684
views
Tool: Molecular Dynamics analysis tools [desmond Schrodinger]
dynamics schrodinger desmond mdanalysis molecular
updated 2.4 years ago by 142k • written 2.4 years ago by • 0
0
votes
0
replies
516
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
10 months ago by Divon ▴ 230
0
votes
0
replies
442
views
Tool: Proteome-pI 2.0 - Proteome Isoelectric Point Database
isoelectric_point protein pKa database proteomics
2.5 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 43k • written 3.2 years ago by ▴ 430
1
vote
1
reply
918
views
Tool: Cell Type Prediction - covering 45 immune cell types
citeseq scRNA singlecell
updated 2.5 years ago by ▴ 50 • written 2.7 years ago by ▴ 580
3
votes
5
replies
2.7k
views
Tool: Extend 3' UTR of a GTF file
annotation python RNA-Seq GTF
updated 10 months ago by 43k • written 3.6 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
597
views
Tool: A pairwise genome alignment pipeline using LAST and Nextflow
genome LAST Nextflow dotplot alignment
2.6 years ago by Charles Plessy ★ 2.9k
0
votes
0
replies
589
views
Tool: NGS-Barcode-Count
DEL NGS CRISPRseq
2.6 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 43k • written 2.6 years ago by ▴ 420
4
votes
0
replies
729
views
Tool: Annoyed by contig name inconsistencies (eg chr22 vs 22)? A solution
contigs bam vcf reference compression
2.6 years ago by Divon ▴ 230
0
votes
0
replies
680
views
Tool: Genotype Imputation Workflow
gwas imputation.
2.6 years ago by nhaus ▴ 360
1
vote
0
replies
495
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 43k • written 2.7 years ago by ▴ 420
1
vote
2
replies
983
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 13 months ago by 43k • 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 43k • 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 43k • written 2.7 years ago by ▴ 420
1
vote
0
replies
517
views
Tool: Looking for feedback on epigenetics R package - enhancer detection and visualization
epigenetics chromatin enhancers atac chip
2.7 years ago by Alex ▴ 20
0
votes
0
replies
560
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
2.7 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 10 months ago by 43k • written 10.6 years ago by ▴ 450
1
vote
0
replies
580
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
9.5k
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 43k • written 3.4 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
551
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
588
views
Tool: Manticore: a software to extract the intermixed regions of subgenomes in hybrid species
mapping hybrid subgenome genomics sequencing
2.8 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 18 months ago by • 0 • written 2.8 years ago by ★ 3.6k
0
votes
0
replies
993
views
Tool: Handy online tool for genomic analysis and data visualization - Part I
NGS Sequencing
updated 13 months ago by 43k • written 2.8 years ago by ▴ 420
2
votes
0
replies
667
views
Tool: metaGEM: create your own genome scale metabolic models directly from metagenomes
metagenomics metagenome-assembled-genome genome-scale-metabolic-model metabolism
updated 2.8 years ago by 43k • written 2.8 years ago by ▴ 20
9
votes
7
replies
3.0k
views
Tool: DiffBind 3.0: Extensive updates in Bioconductor 3.12
DiffBind ChIP-Seq diffbind ATAC-seq chipseq
updated 11 months ago by 43k • written 3.5 years ago by ★ 2.0k
0
votes
1
reply
1.1k
views
Tool: Compi: Application Framework for Portable Computational Pipelines
pipeline workflow-management-system docker
updated 10 months ago by 43k • written 4.6 years ago by ▴ 380
0
votes
0
replies
542
views
Tool: Unicorn Papers - Top ‱ cited papers from PUBMED
citation paper research PUBMED bibliometrics
2.9 years ago by Lukasz Kozlowski • 0
4
votes
7
replies
4.6k
views
6 follow
Tool: MAGERI: a software tool for calling rare variants and detecting circulating tumor DNA from UMI-tagged high-throughput sequencing data
rare-variant resequencing umi ctDNA
updated 12 weeks ago by • 0 • written 7.0 years ago by 3.5k
1
vote
0
replies
596
views
Tool: Super easy to use free paper retrieval artifact: PyPubMed
python pubmed software
updated 10 months ago by 43k • written 3.0 years ago by ▴ 420
734 results • Page 3 of 15
Recent Votes
Answer: Nextflow: how to get the process work dir, within the process
use firehose_get to download TCGA data
Download data from TCGA
Comment: Importing a fastq file
EdgeR - relationship between logFC and coefficients
Answer: EdgeR - relationship between logFC and coefficients
Detecting highly variable genes within replicates
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Popular Question to Amr ▴ 160
Commentator to rpolicastro 13k
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Scholar to Jesse ▴ 770
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Recent Replies
Answer: CNVKIT - unable to produce scatter and diagram pdfs by Anitha • 0
Thank you for the information.
Comment: LncRNA Nomenclature by jain72744 ▴ 10
My data is based on gene counts and the respective gene IDs are given so I should work with ENSGs? lncRNA_transcripts <- getBM(attributes …
Answer: DESeq2 error by ATpoint 82k
At least one group needs replication. That is the short answer. For a longer answer add details on experimental design.
Comment: When should I use R-MarkDown over R-Script ? by ATpoint 82k
Why particular question? Rmarkdown is a composite of markdown and code. You can nicely separate free text, explanation, comments etc. from…
Comment: LncRNA Nomenclature by ATpoint 82k
RNA-seq is typically analyzed on gene rather than transcript level. Are your counts gene or transcript?
Comment: EdgeR - relationship between logFC and coefficients by gBioStar5 ▴ 10
Thanks a lot, this was very helpful. I'll keep that in mind.
Answer: EdgeR - relationship between logFC and coefficients by Gordon Smyth ★ 7.1k
Results presented by topTags() are on the log2 scale. Coefficients stored internally in the DGELRT object are on the loge scale. If you con…
Answer: Importing a fastq file by size_t ▴ 120
run command `explorer.exe .` in wsl terminal, and then drag file to folder
Comment: Contig assembly task, errors by Philipp Bayer 8.4k
Hi Ricardo! CAP3 is an 'older' overlap assembler from 1999 which is perfectly suited for these kinds of 'small' tasks. I used it last in my…
Comment: absolute path for symbolic links in Snakefile by Jesse ▴ 770
That's really handy, and much more of a general solution than stripping off the directory names! So yifangt86, if you're on Linux you can …
Comment: Truncated metadata file report from ENA Portal API by GenoMax 142k
Are you missing a `"` at the end of the URL. Doing wget -O test.out "https://www.ebi.ac.uk/ena/portal/api/filereport?accession=PRJNA43…
Comment: Different output for read length by marco.barr ▴ 100
very strange, I double checked the BAM file and it is the same one I used for your request. Are the commands I wrote above correct? How is …
Comment: Different output for read length by Pierre Lindenbaum 161k
the first read as a length of 1747, i wonder how you can just find '50' $ wget -qO - "https://gist.githubusercontent.com/Macdot3/4650…
Comment: Problem with Seurat package in PercentageFeatureSet function by bk11 ★ 2.4k
Yes, `CreateAssayObject` function is used for only expression matrix.
Comment: Different output for read length by marco.barr ▴ 100
Here is my result, I hope you can see it. [https://gist.github.com/Macdot3/4650243a10540d8c06f728ffc16a136c][1] [1]: https://gist.gith…
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