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News: fastp 0.22 released, with new FASTQ deduplication feature.
fastp
updated 9 months ago by 43k • written 2.7 years ago by ★ 2.5k
2
votes
4
replies
1.5k
views
News: Online training - Snakemake: Reproducible and Scalable Bioinformatic Workflows
Snakemake Pipeline
2.4 years ago by carlopecoraro2 ★ 2.5k
10
votes
4
replies
984
views
News: Good morning
good morning
updated 19 months ago by 100k • written 19 months ago by 87k
1
vote
4
replies
2.0k
views
News: webserver of TCGA data www.tcgaportal.org
genome RNA-Seq TCGA gene
updated 11 months ago by 43k • written 5.9 years ago by ▴ 40
12
votes
4
replies
2.0k
views
News: #NGSchool2018 summer school in bioinformatics
NGSchool Personalised-Medicine Nanopore
updated 11 months ago by 43k • written 5.9 years ago by ▴ 290
2
votes
4
replies
2.0k
views
News: Reminder: Igb Tutorial Starts In 30 Minutes
visualization genome-browser RNA-seq
updated 14 months ago by 43k • written 10.6 years ago by ★ 2.4k
4
votes
4
replies
1.9k
views
News: 12th International Conference on Advancements in Bioinformatics and Drug Discovery
genome Computational-Biology
updated 11 months ago by 43k • written 6.0 years ago by ▴ 20
9
votes
4
replies
1.6k
views
News: Human Cell Atlas Data Coordination Platform Data Release Questionaire
RNA-Seq
updated 11 months ago by 43k • written 6.2 years ago by ★ 1.8k
2
votes
4
replies
1.2k
views
News: Course ONLINE - RNAseq data analysis with R and Bioconductor (15-19 June)
R RNA-seq Bioconductor
updated 10 months ago by 43k • written 4.0 years ago by ★ 2.5k
15
votes
4
replies
2.6k
views
News: Call For Nominations: 2013 Benjamin Franklin Award
benjamin-franklin-award award
updated 14 months ago by 43k • written 11.2 years ago by 161k
15
votes
4
replies
4.7k
views
News: Workshop: Genomic Data Visualization and Interpretation (Berlin, Germany)
dataviz GenVisR next-gen R
updated 12 months ago by 43k • written 7.1 years ago by ★ 2.5k
19
votes
4
replies
2.5k
views
News: How to analyze NGS data: An overview of nine different IT solutions
NGS RNA-Seq DNA-Seq
updated 12 months ago by 43k • written 7.5 years ago by 11k
14
votes
4
replies
3.4k
views
News: FULL: NGS Data Analysis Workshop for Beginners in Munich (29 June - 1 Juli 2016)
RNA-Seq next-gen NGS
updated 21 months ago by 43k • written 8.2 years ago by 11k
4
votes
4
replies
1.7k
views
News: VCFclin working group
vcfclin
updated 13 months ago by 43k • written 10.0 years ago by ▴ 30
6
votes
4
replies
4.3k
views
News: awesome-single-cell: a list of open-source single-cell analysis software and workshop materials
single-cell RNA-Seq
updated 12 months ago by 43k • written 7.8 years ago by 26k
10
votes
4
replies
2.6k
views
News: Ensembl 77 is out
ensembl
updated 2.3 years ago by 43k • written 9.6 years ago by 23k
0
votes
3
replies
1.4k
views
News: :: FINAL CALL :: A Practical Introduction to NGS Data Analysis (Nov 29 - Dec 1, 2023 in Munich, Germany) - only 2 seats left
DNA-Seq NGS RNA-Seq Workshop
5 months ago by David Langenberger 11k
2
votes
3
replies
3.1k
views
News: Summer Course On Analyzing Next-Generation Sequencing Data, June 10-20, Kellog Biological Station, Michigan State University
education
updated 14 months ago by 43k • written 11.2 years ago by 100k
6
votes
3
replies
2.4k
views
News: Become a Professional Biinformatician in NGS, Microarray in very fair price. Register for ArrayGen training program as soon as possible to get good a…
ChIP-Seq next-gen RNA-Seq
updated 12 months ago by 43k • written 7.2 years ago by • 0
4
votes
3
replies
1.9k
views
News: How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications
ChIP-Seq RNA-Seq
updated 12 months ago by 43k • written 7.3 years ago by ▴ 350
5
votes
3
replies
905
views
News: March 13-16: Virtual Nextflow and nf-core training event in 5 languages
nf-core pipeline Nextflow
updated 13 months ago by ▴ 340 • written 14 months ago by 4.5k
20
votes
3
replies
2.7k
views
News: Nature Comment: Core services: Reward bioinformaticians
career-path
updated 22 months ago by 43k • written 9.1 years ago by ★ 2.2k
12
votes
3
replies
2.5k
views
News: Google Summer of Code and Open Bioinformatics Foundation is looking for students
GSoC open-source
updated 12 months ago by 43k • written 8.1 years ago by 8.3k
3
votes
3
replies
1.2k
views
News: NCBI's IgBLAST version 1.21.0 is now available
IgBLAST BLAST T-Cell NCBI receptors
11 months ago by PeterC_NCBI ▴ 410
2
votes
3
replies
1.7k
views
News: GCCBOSC 2018: A Bioinformatics Community Conference Call for Abstracts
Galaxy-Community-Conference BOSC GCC
updated 11 months ago by 43k • written 6.2 years ago by ★ 2.2k
3
votes
3
replies
2.3k
views
News: Innocentive Challenge: Identify Organisms From A Stream Of Dna Sequences And Get $1,000,000
ngs
updated 14 months ago by 43k • written 11.0 years ago by ▴ 830
0
votes
3
replies
1.0k
views
News: EMBO | EMBL Symposium: Seeing is Believing - Imaging the Molecular Processes of Life
image-analysis
updated 11 months ago by 43k • written 5.5 years ago by ▴ 10
2
votes
3
replies
2.1k
views
News: PDX Models: Tumor-stroma interaction
transcriptome pdx R ChIP-Seq
updated 11 months ago by 43k • written 6.8 years ago by ▴ 70
0
votes
3
replies
2.8k
views
News: Physalia-courses: 16S rRNA gene Metabarcoding Workshop
RNA-seq sequencing SNP gene sequence
updated 12 months ago by 43k • written 7.5 years ago by ★ 2.5k
0
votes
3
replies
874
views
News: NCBI update complete. Aspera users please update your client.
NCBI Submissions GenBank
14 months ago by PeterC_NCBI ▴ 410
0
votes
3
replies
2.4k
views
News: Eukaryotic Metabarcoding workshop
next-gen blast alignment
updated 12 months ago by 43k • written 7.4 years ago by ★ 2.5k
0
votes
3
replies
1.1k
views
News: Nvidia Clara Parabricks is FREE for R&D
nvidia workflow gpu
updated 16 months ago by 2.8k • written 16 months ago by 161k
18
votes
3
replies
2.5k
views
News: LAST CALL: Next-Generation Sequencing Data Analysis: A Practical Introduction (Frankfurt, Germany) - 2 seats left
DNA-Seq NGS Workshop Variant-Calling
updated 21 months ago by 43k • written 7.2 years ago by 11k
9
votes
3
replies
4.8k
views
News: Bioinformatics Contest 2020. Call for problems
contest
updated 10 months ago by 43k • written 4.6 years ago by ▴ 920
1
vote
3
replies
917
views
News: NCBI BLAST ClusteredNR database now available for blastx and PSI-BLAST searches
PSI-BLAST blastx BLAST NCBI ClusteredNR
15 months ago by PeterC_NCBI ▴ 410
4
votes
3
replies
1.9k
views
News: Proteomics and Genomics Submit your Research Journals
Research Genomics Journals Proteomics
updated 17 months ago by 43k • written 8.8 years ago by • 0
7
votes
3
replies
1.9k
views
News: New NCBI Datasets home and documentation pages provide easier access
ncbi gene SARS-CoV-2 genome
updated 3.0 years ago by 100k • written 3.0 years ago by ▴ 50
7
votes
3
replies
3.9k
views
News: Visualizing genomic data: techniques and challenges. Our interview with Dr. Malachi Griffith, Dr. Obi Griffith and Mr. Zachary Skidmore (The Griffith…
R RNA-Seq genome NGSdata
updated 11 months ago by 43k • written 6.8 years ago by ★ 2.5k
1
vote
3
replies
1.2k
views
News: 4th Berlin Summer School in NGS Data Analysis - October 5-9, 2020
NGS RNA-Seq DNA-Seq
updated 10 months ago by 43k • written 4.2 years ago by 11k
0
votes
3
replies
2.2k
views
News: Bioinformatics National Certification Examination (BINC)
BINC
updated 12 months ago by 43k • written 8.0 years ago by • 0
2
votes
3
replies
1.4k
views
News: Bio-On-Magnetic-Beads (BOMB): Open platform for high-throughput nucleic acid extraction and manipulation
rna-extraction dna-extraction rna-seq
updated 11 months ago by 43k • written 5.6 years ago by ▴ 20
4
votes
3
replies
1.0k
views
News: You may need to cleanup duplicate NCBI BLAST nt database volumes on your system
databases NCBI BLAST
8 months ago by PeterC_NCBI ▴ 410
4
votes
3
replies
3.3k
views
News: CAFE v4.0 available
phylogenetics CAFE
updated 11 months ago by 43k • written 7.1 years ago by ▴ 150
7
votes
3
replies
4.6k
views
News: Pathway Commons 2 - Search And Visualize Public Biological Pathway Information. Single Point Of Access.
api cytoscape
updated 14 months ago by 43k • written 10.4 years ago by ★ 1.2k
4
votes
3
replies
1.9k
views
News: Boston Genomics Hackathon (facilitated by NCBI)
NCBI RNA-Seq DNA-seq hackathon
updated 12 months ago by 43k • written 8.1 years ago by ▴ 330
22
votes
3
replies
3.0k
views
News: Biostar: 10,000 Question Milestone
meta
updated 14 months ago by 43k • written 10.9 years ago by 100k
2
votes
3
replies
710
views
News: NCBI Comparative Genome Viewer now allows searches for genes across aligned assemblies
Browser NCBI Alignments Genome
16 months ago by PeterC_NCBI ▴ 410
4
votes
3
replies
3.2k
views
News: -max_target_seqs 1 in NCBI standalone BLAST does not do what you think it does
blast
updated 11 months ago by 43k • written 5.5 years ago by 11k
3
votes
3
replies
3.9k
views
News: A Tale Of Next Generation Sequencing Platforms: Ion Torrent, Pacific Biosciences And Illumina Miseq
sequencing
updated 14 months ago by 43k • written 11.7 years ago by 100k
3
votes
3
replies
1.0k
views
News: Want to automate your NGS analyses and create reproducible/scalable pipelines? Join our hands-on Nextflow workshop!
nextflow NGS pipeline
2.0 years ago by David Langenberger 11k
1,000 results • Page 3 of 20
Recent Votes
A: Blast Settings For Short Sequences
A: Blast Settings For Short Sequences
Comment: Heatmap and rna-seq
Answer: Heatmap and rna-seq
Comment: Heatmap and rna-seq
A: should FASTA files be sorted before indexed with SAMtools?
Answer: A faidx-indexed FASTA format file or a FASTA format file
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Scholar to Alex Reynolds 35k
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Recent Replies
Answer: Limma Analysis Agilent Microarray Data (GPL1708) by Gordon Smyth ★ 7.0k
There is an Agilent array case study in the limma User's Guide, which you might find helpful and somewhat simpler. I don't recommend col…
Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR? by Gordon Smyth ★ 7.0k
The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1. Have you exam…
Answer: How to use limma to find differentially expressed genes in response to a continu by Gordon Smyth ★ 7.0k
There's no need for form a contrast because the score variable is already in the model. A continuous variable is its own contrast. Just run…
Comment: Create a new bed file with all pairwise combinations between two other bed files by J ▴ 10
Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files by J ▴ 10
Thank you Pierre! I'll try this out with my full data set.
Answer: DNA methylation preprocessing by cao510927 ▴ 30
I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
Answer: Create a new bed file with all pairwise combinations between two other bed files by Alex Reynolds 35k
I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
Comment: Highest variable features in single cell data by bk11 ★ 2.4k
You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
Comment: Heatmap and rna-seq by GenoMax 141k
Please include a link when you are recommending a tool. There can be programs with similar names.
Answer: Heatmap and rna-seq by dsull ★ 5.8k
Check out clustergrammer from Avi Ma'ayan's lab.
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by Ram 43k
Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i by ATpoint 82k
You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by BioinfGuru ★ 1.7k
Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
Comment: Low mapping rate with Salmon by i.sudbery 19k
Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
Comment: How to convert plink files to Hapmap Format by bk11 ★ 2.4k
If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value. https://www.b…
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