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733 results • Page 3 of 15
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2
votes
0
replies
592
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
604
views
Tool: New VCF Header (schema) Parser---Please Break!!!
VCF header
updated 2.1 years ago by ★ 2.9k • written 2.1 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 19k
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
466
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
479
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 5.2 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
683
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
514
views
Tool: SBGNview published online with Bioinformatics
Pathview BioConductor SBNGview visualization pathway
2.4 years ago by bigmawen ▴ 430
10
votes
5
replies
2.4k
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 10 months ago by 43k • written 3.2 years ago by ▴ 430
1
vote
1
reply
916
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
596
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
588
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 14 months ago by 43k • written 2.6 years ago by ▴ 420
4
votes
0
replies
726
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 ▴ 310
1
vote
0
replies
495
views
Tool: shell script to search txt in academic figures
search_txt_in_image.sh
2.6 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 14 months ago by 43k • written 2.6 years ago by ▴ 420
1
vote
2
replies
981
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
515
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
559
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
9.4k
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 10 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
549
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
587
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
991
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
2.9k
views
Tool: DiffBind 3.0: Extensive updates in Bioconductor 3.12
DiffBind ChIP-Seq diffbind ATAC-seq chipseq
updated 10 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 4.5 years ago by ▴ 380
0
votes
0
replies
540
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 11 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 2.9 years ago by ▴ 420
0
votes
0
replies
678
views
Tool: Help solve the cancer puzzle & benefit your research! SimBioSys PhenoScope for integrative multi-modal and multi-omic data analytics
multi-modal multi-omic breast analytics cancer imaging
2.9 years ago by johnpfeiffer • 0
733 results • Page 3 of 15
Recent Votes
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
A: After read mapping, count exons or genes?
After read mapping, count exons or genes?
Merging a large number of VCF files
A: Merging a large number of VCF files
A: pulling snps from vcf file using ids
pulling snps from vcf file using ids
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Popular Question to SHN ▴ 40
Popular Question to Rob ▴ 170
Scholar to GenoMax 142k
Popular Question to curious ▴ 750
Popular Question to M. ▴ 30
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Recent Replies
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…
Comment: The GDC Legacy Archive is retiring soon. by lcordeiro ▴ 40
Hi Zhenyu, do you happen to know how I can download metadata for some of the legacy files? I downloaded several IDATs from the legacy data …
Answer: Force PLINK2 to neglect chrX as the sex chromosome by chrchang523 10k
(cross-posted from https://groups.google.com/g/plink2-users/c/Qphx_6BpPII ) You need to use --chr-set, not --allow-extra-chr, to specify…
Answer: Easy way to find out which allele is minor allele from bed file? by chrchang523 10k
This question does not make sense. If you care about allele-order "information [being] lost in downstream applications", REF/ALT is the ob…
Answer: visualize GSEA by bk11 ★ 2.4k
I have made some edits in your code basically changing the position of text and commented out the line `data$text_pos <- ifelse(data$NES > …
Comment: Differential Expression Analysis using DESeq2 in R by swbarnes2 14k
Pictures of code are useless. You were told to paste the code and use the 0101 button. Can you explain why you decided not to do that? If…
Comment: Differential Expression Analysis using DESeq2 in R by Erina • 0
![Here is the code I am using for the analysis][1] [1]: /media/images/8a511904-6ae8-47f5-b647-ee15b02b
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read by swbarnes2 14k
In paired end sequencing, every read has a mate, and the flags all together tell you not only what is up with the read you are looking at, …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by Mbofire • 0
I need assistance don't know what to do next after signing up
Comment: Easy way to find out which allele is minor allele from bed file? by curious ▴ 750
According to the link: "When *generating* such filesets, PLINK 1.x defaults to swapping the alleles whenever A1's frequency is above (not …
Comment: TaxID mapping file by GenoMax 142k
nodesDB file should have been installed if you had used "Install" script for `blobtools` according to : https://blobtools.readme.io/docs/ta…
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