Limit : all time
all time today this week this month this year
734 results • Page 3 of 15
Sort: Views
Rank Views Votes Replies
27
votes
13
replies
6.0k
views
Tool: DEA.R: Command line script for differential expression analysis with R packages (DESeq2/edgeR/limma-voom)
edgeR DESeq2 limma RNA-Seq
updated 10 months ago by 43k • written 7.8 years ago by 47k
9
votes
4
replies
5.9k
views
Tool: BPGA - Bacterial Pan Genome Analysis pipeline
sequence genome comparative-genomics bacteria
updated 10 months ago by 43k • written 8.0 years ago by ▴ 80
5
votes
3
replies
5.9k
views
Tool: CRAVAT: a web tool to annotate and analyze cancer variants
sequencing variant annotation Cancer
updated 2.3 years ago by 43k • written 8.6 years ago by ▴ 1000
8
votes
6
replies
5.9k
views
Tool: chromoMap- R package for Interactive visualization and Annotation of chromosomes or regions of any living organism.
annotation R genome visualization
updated 11 months ago by 43k • written 5.1 years ago by ▴ 80
4
votes
6
replies
5.8k
views
Tool: Fungal genome annotation
genome sequencing
updated 2.4 years ago by 43k • written 9.3 years ago by ▴ 90
10
votes
0
replies
5.8k
views
Tool: Shell utilities for QC of FASTQ/FASTA files (based on perl one-liners)
PERL GNUPLOT FASTA FASTQ FastQC
updated 10 months ago by 43k • written 10.1 years ago by ★ 1.8k
4
votes
3
replies
5.8k
views
Tool: KeggExp: a web server for visualizing KEGG pathways maps when analyzing expression profile data
expression-profile-data pathway-visualization
9 months ago by liux.bio ▴ 360
10
votes
6
replies
5.7k
views
Tool: Shell script to automate trimmomatic for multiple samples
bash shell trimmomatic
updated 10 months ago by 43k • written 5.0 years ago by 5.8k
3
votes
4
replies
5.7k
views
Tool: ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases.
ngs.plot NGS-data visualize
updated 14 months ago by 43k • written 10.0 years ago by ▴ 650
53
votes
13
replies
5.7k
views
6 follow
Tool: I made a DNA/gene/bioinformatics-y workshop for 11-16 year olds which people may find useful
school-outreach
updated 16 months ago by 43k • written 9.0 years ago by ★ 4.0k
6
votes
0
replies
5.6k
views
Tool: cnv_facets: somatic Copy Number Variant calling using the facets package
CNV somatic facets cancer
updated 10 months ago by 43k • written 5.4 years ago by 14k
7
votes
5
replies
5.6k
views
Tool: XENA: a new tool for cancer researcher developed by UCSC
ucsc visualization cancer
updated 10 months ago by 43k • written 8.7 years ago by ★ 5.2k
4
votes
5
replies
5.5k
views
Tool: Blob.js - a small javascript library to draw random blobs/shapes
javascript html figure
updated 21 months ago by 43k • written 8.5 years ago by ★ 1.2k
1
vote
2
replies
5.4k
views
Tool: TCGA & METABRIC Breast Cancer Subtype Survival Curve
gene RNA-Seq
updated 10 months ago by 43k • written 6.9 years ago by ▴ 40
9
votes
3
replies
5.4k
views
Tool: Luigi's Monkey Wrench - A small helper library for commandline heavy bioinformatics workflows in Spotify's Luigi workflow tool
workflows luigi python command-line
updated 2.0 years ago by 43k • written 9.2 years ago by ★ 1.3k
2
votes
0
replies
5.4k
views
Tool: NGS Data Analysis Pipeline for Virus Identification
virus
updated 22 months ago by 43k • written 9.1 years ago by ▴ 70
19
votes
2
replies
5.3k
views
Tool: CIViC - Clinical Interpretation of Variants in Cancer
clinical-interpretation civic variant cancer
updated 10 months ago by 43k • written 9.2 years ago by 20k
4
votes
6
replies
5.3k
views
Tool: NtSeq: JavaScript bioinformatics library for nucleotide sequence manipulation and analysis.
alignment JavaScript sequence
updated 2.1 years ago by 43k • written 9.3 years ago by ▴ 60
7
votes
0
replies
5.3k
views
Tool: Gem: Genome Wide Event Finding And Motif Discovery
motif
updated 10 months ago by 43k • written 11.5 years ago by 6.0k
26
votes
4
replies
5.3k
views
Tool: Dgidb - Mining The Druggable Genome
dgidb drug-gene-interaction
updated 10 months ago by 43k • written 10.6 years ago by 20k
11
votes
2
replies
5.3k
views
Tool: ChIPQC: a package for assessing quality of ChIP-seq samples and experiments
quality-control quality-assessment ChIP-Seq
updated 10 months ago by 43k • written 10.1 years ago by ★ 2.0k
5
votes
4
replies
5.3k
views
Tool: Contiguator: A Bacterial Genomes Finishing Tool For Structural Insights On Draft Genomes
reference-genome contigs
updated 10 months ago by 43k • written 11.9 years ago by ▴ 770
6
votes
4
replies
5.2k
views
Tool: Sorting bed files with bash sort
bash bed
updated 13 months ago by 43k • written 8.8 years ago by ★ 2.5k
2
votes
6
replies
5.2k
views
Tool: Variantannotation Package (Bioconductor)
snp variant-annotation
updated 10 months ago by 43k • written 11.8 years ago by 20k
13
votes
6
replies
5.2k
views
Tool: csvtk - a cross-platform, efficient, practical and pretty CSV/TSV toolkit
CSV Golang TSV
9 months ago by shenwei356 8.5k
7
votes
17
replies
5.1k
views
Tool: SPLiT-Seq Demultiplexing a bash tool for extraction of barcoded single cells
RNA-Seq sequencing
updated 10 months ago by 43k • written 5.7 years ago by ▴ 80
56
votes
23
replies
5.1k
views
10 follow
Tool: ASCIIGenome: Text Only Genome Viewer!
terminal genome-browser java ASCIIGenome
updated 10 months ago by 43k • written 7.8 years ago by 14k
28
votes
17
replies
5.1k
views
7 follow
Tool: PCAtools: everything Principal Components Analysis
eigenvector pca bioconductor R
updated 11 months ago by 43k • written 5.3 years ago by 88k
7
votes
6
replies
5.1k
views
Tool: mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
depth-of-coverage exome WGS
updated 10 months ago by 43k • written 6.3 years ago by 24k
3
votes
0
replies
5.0k
views
Tool: GUI for MrBayes
Phylogenetic-analyses MrBayes Bayesian-inference
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 110
2
votes
0
replies
5.0k
views
Tool: Prodigal: Prokaryotic Dynamic Programming Genefinding Algorithm For Microbial Genomes
annotation
updated 10 months ago by 43k • written 11.7 years ago by 100k
3
votes
5
replies
5.0k
views
Tool: Phevor: Phenotype Driven Variant Ontological Re-Ranking Tool
interpretation prioritization phevor vaast
updated 10 months ago by 43k • written 9.9 years ago by ▴ 30
25
votes
3
replies
5.0k
views
Tool: Quick statistics from the command line
statistics C
updated 17 months ago by 43k • written 8.9 years ago by ★ 2.3k
5
votes
5
replies
4.9k
views
Tool: Mutect: Accurate Identification Of Somatic Point Mutations
mutect
updated 10 months ago by 43k • written 12.1 years ago by 11k
8
votes
0
replies
4.9k
views
Tool: shinyCircos: an R/shiny application for creation of Circos plot interactively
Circos R Shiny Genome
updated 10 months ago by 43k • written 5.8 years ago by ▴ 110
3
votes
15
replies
4.9k
views
Tool: Annocript: completely automated transcriptome annotation pipeline which can also identify putative lncRNAs
annotation RNA-Seq
updated 2.0 years ago by 43k • written 9.2 years ago by ▴ 70
2
votes
2
replies
4.9k
views
Tool: Budapest Reference Connectome: a 3D visualization tool to browse connections in the human brain
connectome neuroscience brain
updated 15 months ago by 43k • written 9.0 years ago by ▴ 350
1
vote
2
replies
4.9k
views
Tool: Genetalk - A Platform To Analyse Your Genetic Variant Data And Talk About It
vcf
updated 10 months ago by 43k • written 10.7 years ago by ▴ 130
6
votes
3
replies
4.9k
views
Tool: Clustering of short peptide sequences
peptide phage-display clustering
updated 20 months ago by 43k • written 8.6 years ago by ▴ 420
1
vote
0
replies
4.9k
views
Tool: diffpdb - a simple tool to compare text-content of PDB files
structural-bioinformatics diff pdb-format
updated 22 months ago by 43k • written 9.1 years ago by ▴ 150
11
votes
12
replies
4.9k
views
Tool: Mapsembler2 targeted micro assembly and visualization of the local assembly graph
minia mapsembler next-gen Assembly
updated 2.1 years ago by 43k • written 9.8 years ago by ▴ 900
22
votes
20
replies
4.9k
views
Tool: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
sam bam bqsr
updated 11 months ago by 43k • written 5.6 years ago by ▴ 150
13
votes
6
replies
4.9k
views
Tool: GAWN - Genome Annotation Without Nightmares
genome-annotation
updated 10 months ago by 43k • written 6.8 years ago by 11k
6
votes
8
replies
4.9k
views
Tool: Read-based phasing with WhatsHap
phasing
updated 10 months ago by 43k • written 7.4 years ago by ▴ 100
18
votes
6
replies
4.8k
views
Tool: R code for ecological data analysis
next-gen R Metagenomics
updated 2.1 years ago by 43k • written 9.3 years ago by ★ 1.8k
3
votes
5
replies
4.8k
views
Tool: Omicia Opal Research - Variant Annotation and Disease-Gene Prioritization
annotation interpretation vaast
updated 10 months ago by 43k • written 9.9 years ago by ▴ 30
11
votes
1
reply
4.8k
views
Tool: Ideogram.js: a JavaScript library for chromosome visualization
javascript chromosome visualization ideogram
updated 10 months ago by 43k • written 6.1 years ago by ▴ 120
6
votes
6
replies
4.8k
views
Tool: Reading/ Writing FASTA files in Java
FASTA Java
updated 10 months ago by 43k • written 9.4 years ago by • 0
6
votes
2
replies
4.8k
views
Tool: Snpeff - Annotating And Predicting The Effects Of Single Nucleotide Polymorphisms
snp variant-annotation
updated 10 months ago by 43k • written 11.8 years ago by 20k
12
votes
0
replies
4.8k
views
Tool: UMI-Tools 0.5, now with tools for cell barcoded scRNA-seq
UMI RNA-Seq single-cell
updated 10 months ago by 43k • written 6.7 years ago by 19k
734 results • Page 3 of 15
Recent Votes
The Biostar Handbook. A bioinformatics e-book for beginners.
The Biostar Handbook. A bioinformatics e-book for beginners.
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
What is Deepvariant default filtering values ?
Answer: Filtering Multi-sample VCF file for all except one Genotype
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax?
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
Recent Locations • All
Turkey, just now
Egypt, 1 minute ago
Spain, 2 minutes ago
Iran, 5 minutes ago
Russian Federation, 7 minutes ago
France, 7 minutes ago
Hong Kong, 7 minutes ago
Recent Awards • All
Popular Question to rj.rezwan • 0
Popular Question to matteo.levorato • 0
Popular Question to Palgrave ▴ 110
Popular Question to DBScan ▴ 300
Popular Question to chrisk • 0
Popular Question to mbrav005 • 0
Popular Question to Sofia • 0
Recent Replies
Answer: Duplicated reads (IDs) from nanopore sequencing by marco.barr ▴ 110
Hi, I'm also working with ONT data and with dorado. From experience I tell you that some versions of MInKNOW have bad management of fast5 f…
Comment: Problem with Calling Variants from RNA-Seq data by Esraa • 0
Yes, i specifically ran the RNA-seq best practices, and no i have not taken RNA editing into account considering this is not mentioned in t…
Comment: Problem with Calling Variants from RNA-Seq data by i.sudbery 19k
Have you accounted for A>I RNA editing?
Comment: Problem with Calling Variants from RNA-Seq data by Esraa • 0
**My references** Genome: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/references/GRCh38/GCA_000001405.15_GRCh38_no_al…
Answer: Getting differential ChIP-seq peaks between conditions after calling consensus p by ATpoint 82k
This has formally been investiated by a reputable group here: https://academic.oup.com/nar/article/42/11/e95/1442937 IIRC they think tha…
Comment: RNA seq analysis by Jacek ▴ 10
Thank you so much Matthias this is really helpful, I got insight from this. Have a nice day
Answer: Differential Expression with limma: Contrast and Design Matrix, combinatorial ap by dariober 14k
> Is this a statistically valid approach to compare the impact of any bacterial exposure and genotype? At a glance, it seems fine to me…
Comment: Filtering Multi-sample VCF file for all except one Genotype by Pierre Lindenbaum 161k
> 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…
Answer: Filtering VCF files based on VAF giving incorrect results by Pierre Lindenbaum 161k
using vcfilterjdk: https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/ java -jar ${JVARKIT_DIST}/jvarkit.jar vcffilterjdk …
Comment: Applying the metacell2 algorithm using python by JACKY ▴ 140
I have one more question please. When reading the h5ad file at the very beginning, do I need to perform the usual scanpy normalization step…
Comment: Using Cutadapt to trim adapters from paired-end small RNA sequence data by melissa.joubert • 0
Thank you! This was going to be my next option - to simply use the Read_1 libraries for all samples. Can I ask about the second option you…
Comment: Filtering Multi-sample VCF file for all except one Genotype by schmince • 0
Thanks, that was exactly what i needed
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads) by Esraa • 0
Thank you! I will try searching for this more and see if it would fit my analysis purposes.
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads) by Esraa • 0
Thank you so much for answering! I actually found some studies doing it the way you mentioned. I ran the GATK best practices pipeline on t…
Comment: BWA alignment by a.alnawfal.1992 ▴ 260
that's great, but i believe the issue is related to stdin rather than index
Traffic: 2327 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6