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News: Google Dataset Search
google
updated 11 months ago by 43k • written 5.6 years ago by 161k
5
votes
0
replies
992
views
News: Free online Ensembl REST API training
perl rest-api jupyter python ensembl
updated 11 months ago by 43k • written 5.4 years ago by 23k
5
votes
0
replies
1.8k
views
News: Bioinformatics Contest 2019
bioinforussia bioinfcontest bioinfcontest2019
updated 11 months ago by 43k • written 5.4 years ago by ▴ 50
4
votes
0
replies
720
views
News: Call for Bioinformatics Papers - Genes Special Issue
gene
updated 10 months ago by 43k • written 4.3 years ago by ▴ 730
4
votes
2
replies
1.3k
views
News: Hands-On Workshop: How to use bisulfite-treated sequencing to study DNA methylation (BS-Seq, Bisulfite-Seq, WGBS)
Workshop methylation bisulfite
updated 10 months ago by 43k • written 4.6 years ago by ★ 1.0k
4
votes
0
replies
1.0k
views
News: SIG Workshop to discuss developments in computational pathology and its interfacing opportunities with bioinformatics during ECCB 2018
microscopy wsi digital-pathology
updated 11 months ago by 43k • written 5.7 years ago by ▴ 40
4
votes
0
replies
1.9k
views
News: Bioinformatics education: biology-inspired bioinformatics with project-based learning
education RNA-seq
updated 11 months ago by 43k • written 6.1 years ago by ▴ 340
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
4
votes
2
replies
595
views
News: Standalone NCBI ClusteredNR database now available for download
ClusteredNR NCBI standalone BLAST
7 months ago by PeterC_NCBI ▴ 410
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
0
replies
1.2k
views
News: Workshop for genomic data visualization and interpretation
R RNA-Seq ggplot2 genomics
updated 11 months ago by 43k • written 5.4 years ago by 19k
4
votes
0
replies
645
views
News: A Practical Introduction to Single-Cell RNA-Seq Data Analysis (November 8-10, 2023 in Berlin, Germany)
NGS RNA-Seq single-cell workshop
10 months ago by David Langenberger 11k
4
votes
2
replies
2.9k
views
News: New ebook: From cell line to Command line to learn computational biology
unix snakemake computational-biology RNA-seq
5 months ago by Ming Tommy Tang ★ 3.9k
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
4
votes
0
replies
200
views
News: Transform Your Research with Our NGS Data Analysis Online Course!
DNAseq NGS Biologists OnlineCourse RNAseq
3 months ago by David Langenberger 11k
4
votes
0
replies
1.4k
views
News: ONLINE course - Metagenomics, metatranscriptomics, and multi'omics for microbial community studies
next-gen-sequencing
updated 10 months ago by 43k • written 4.1 years ago by ★ 2.5k
4
votes
0
replies
1.1k
views
News: 2nd edition of the WORKSHOP on Genomic Data Visualization and Interpretation
R BioConductor DataViz
updated 11 months ago by 43k • written 5.6 years ago by ★ 2.5k
4
votes
0
replies
1.5k
views
News: All of Us (NIH) precision medicine research program is now open for enrollment
precision-medicine
updated 11 months ago by 43k • written 6.0 years ago by 141k
4
votes
1
reply
1.8k
views
News: scRNA-seq data analysis Workshop in Berlin
RNA-Seq next-gen
updated 11 months ago by 43k • written 5.5 years ago by ★ 2.5k
4
votes
1
reply
1.2k
views
News: Bioinformatics Workflows with Nextflow
Netflow reproducibility Workflows
updated 10 months ago by 43k • written 4.4 years ago by ★ 2.5k
4
votes
1
reply
1.8k
views
News: Bioinformatics Contest 2018
contest
updated 11 months ago by 43k • written 6.3 years ago by ▴ 40
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
4
votes
0
replies
4.0k
views
News: RepurposeDB - A New Reference Database of Drug Repositioning
precision-medicine drug-repositioning
updated 11 months ago by 43k • written 7.1 years ago by 18k
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
3
votes
0
replies
1.9k
views
News: Deep learning in GATK4
GATK4 deep-learning GATK
updated 11 months ago by 43k • written 6.3 years ago by ★ 1.2k
3
votes
2
replies
1.3k
views
News: Genome Informatics meeting software list
meetings genomics informatics software
updated 11 months ago by 43k • written 6.5 years ago by 26k
3
votes
2
replies
736
views
News: NCBI BLAST+ 2.14.1 Now Available
NCBI BLAST
8 months ago by PeterC_NCBI ▴ 410
3
votes
0
replies
118
views
News: Interested in Spatial Omics?
Bioconductor Spatial-Omics Spatial-Transcriptomics
updated 3 days ago by 43k • written 3 days ago by ★ 2.5k
3
votes
0
replies
710
views
News: Testing and feedback of upcoming salmon release
salmon RNA-Seq
updated 10 months ago by 43k • written 4.6 years ago by 6.5k
3
votes
0
replies
1.3k
views
News: Nextflow Training Course
Pipeline Workflow NEXTFLOW
updated 10 months ago by 43k • written 4.6 years ago by ★ 2.5k
3
votes
0
replies
298
views
News: NCBI BLAST+ 2.2.15 now available for download
NCBI Taxonomy BLAST
5 months ago by PeterC_NCBI ▴ 410
3
votes
2
replies
1.0k
views
News: BETA Testing Opportunity for new RNA-seq data analysis tool
beta-testing RNA-seq multi-omics ngs
updated 11 months ago by 43k • written 5.3 years ago by • 0
3
votes
5
replies
1.3k
views
News: Ensembl Release 104 and newer GTF files no longer have genes sorted by position
Ensembl GTF
updated 7 months ago by ▴ 120 • written 17 months ago by ▴ 30
3
votes
0
replies
1.0k
views
News: Invitation to submit articles to the Bioconductor Gateway on F1000Research
bioconductor
updated 11 months ago by 43k • written 6.1 years ago by 26k
3
votes
1
reply
1.5k
views
News: Bioconductor 2017 Conference, Boston, July 26-28
R conference Bioconductor
updated 11 months ago by 43k • written 7.1 years ago by 26k
3
votes
0
replies
1.9k
views
News: Free Training in Bioinformatic analysis available with Pine Biotech T-BioInfo
RNA-Seq biotech next-gen-sequencing
updated 11 months ago by 43k • written 6.8 years ago by ▴ 70
3
votes
0
replies
784
views
News: ::FINAL CALL:: NGS Data Analysis for Beginners - 11-13 December 2019 in Munich, Germany (2 seats left)
NGS Workshop
updated 10 months ago by 43k • written 4.5 years ago by 11k
3
votes
1
reply
841
views
News: PrecisionFDA has won a FedHealth IT award!!
platform cloud-based precision-medicine award
updated 11 months ago by 43k • written 4.9 years ago by ▴ 150
3
votes
0
replies
1.0k
views
News: Free online Ensembl course
webinar Ensembl mooc training online
updated 11 months ago by 43k • written 5.7 years ago by 23k
3
votes
1
reply
6.8k
views
News: LinkedOmics - a web portal for TCGA/CPTAC data
TCGA cptac cancer
updated 11 months ago by 43k • written 6.4 years ago by 141k
3
votes
0
replies
92
views
News: Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy Generative-AI scRNA Machine-Learning
updated 2 hours ago by 43k • written 13 hours ago by ▴ 60
3
votes
0
replies
1.8k
views
News: New web BLAST default parameters and search limits are now in place at NCBI
www-blast blast ncbi
updated 10 months ago by 43k • written 3.9 years ago by 141k
3
votes
0
replies
1.3k
views
News: Course on Programming for Evolutionary Biology
Evolution R genome Python
updated 11 months ago by 43k • written 5.4 years ago by ★ 2.2k
3
votes
1
reply
1.4k
views
News: Ensembl in Google Summer of Code
Ensembl Internship Google-Summer-of-Code GSOC
updated 11 months ago by 43k • written 7.1 years ago by 23k
3
votes
1
reply
1.4k
views
News: GATK returns to a fully open-source license
gatk
updated 11 months ago by 43k • written 6.9 years ago by 100k
3
votes
0
replies
546
views
News: gnomAD v4 released
gnomad
5 months ago by Pierre Lindenbaum 161k
3
votes
1
reply
2.3k
views
News: NCBI : New API Keys for the E-utilities
pubmed eutils ncbi api
updated 11 months ago by 43k • written 6.5 years ago by 161k
3
votes
0
replies
1.4k
views
News: NIH Strategic Plan for Data Science
nih data-science
updated 11 months ago by 43k • written 6.1 years ago by 141k
3
votes
1
reply
950
views
News: Results are now available for the precisionFDA NCI-CPTAC Multi-omics Enabled Sample Mislabeling Correction Challenge!
precisionFDA NCI challenge algorithm multi-omics
updated 11 months ago by 43k • written 5.2 years ago by ▴ 60
3
votes
1
reply
1.2k
views
News: UniProt: Change of FT and CC section in UniProtKB text format
uniprot protein
updated 10 months ago by 43k • written 4.6 years ago by ★ 2.4k
900 results • Page 2 of 18
Recent Votes
A: should FASTA files be sorted before indexed with SAMtools?
Answer: A faidx-indexed FASTA format file or a FASTA format file
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
Comment: Create a new bed file with all pairwise combinations between two other bed files
Answer: Create a new bed file with all pairwise combinations between two other bed files
Answer: Create a new bed file with all pairwise combinations between two other bed files
Answer: Create a new bed file with all pairwise combinations between two other bed files
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Scholar to Alex Reynolds 35k
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Recent Replies
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…
Comment: genome assembly records not present in assembly_summary.txt by sapuizait ▴ 10
jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Comment: ScRNA data question by bk11 ★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
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