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7
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News: Ncbi E-Utilities Now Provides Output In Json Format (Einfo, Esearch, And Esummary Only, For Now)
ncbi format eutils entrez
updated 9 months ago by 39k • written 9.3 years ago by 154k
9
votes
3
replies
3.0k
views
News: New Human Genome Assembly (Grch38) Released
human-genome assembly
updated 3 months ago by 39k • written 9.4 years ago by 154k
0
votes
1
reply
3.0k
views
News: Call For Book Chapters: Big Data Analytics in Genomics (Springer USA)
Book-Chapter CFP
updated 9 months ago by 39k • written 7.6 years ago by ▴ 10
0
votes
0
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3.0k
views
News: sRNAbench: profiling of small RNAs and its sequence variants in single or multi-species high-throughput experiments
webserver isomiRs microRNA small-RNA
updated 12 weeks ago by 39k • written 8.6 years ago by 9.9k
4
votes
3
replies
3.0k
views
News: CAFE v4.0 available
phylogenetics CAFE
updated 21 days ago by 39k • written 6.2 years ago by ▴ 150
3
votes
0
replies
3.0k
views
News: Tumorportal - A Tool For Exploring A Pan-Cancer Dataset
tcga cancer-genomics
updated 3 months ago by 39k • written 9.3 years ago by 19k
12
votes
8
replies
3.0k
views
News: 'Potential Rna-Dna Binding Site In Alu Repeat', Or 'Why Should I Allow Multiple Mapping Positions When Analyzing Chipseq Data?'
chipseq rna
updated 3 months ago by 39k • written 9.9 years ago by 9.9k
2
votes
0
replies
3.0k
views
News: Short Course And Workshop On Rna-Seq Analysis
RNA-seq
updated 3 months ago by 39k • written 9.4 years ago by ▴ 60
7
votes
1
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2.9k
views
News: A Multi-Split Mapping Algorithm For Circular Rna, Splicing, Trans-Splicing, And Fusion Detection
ngs mapping
updated 3 months ago by 39k • written 9.3 years ago by 9.9k
2
votes
2
replies
2.9k
views
News: Upcoming Hands-On NGS Data Analysis Workshops 2018
Mapping Workshop RNA-Seq Quality-Control DNA-Seq
updated 15 days ago by 39k • written 5.5 years ago by 9.9k
10
votes
1
reply
2.9k
views
News: Ucsc: Dna Sequences In Web Pages Indexed By Bing.Com / Microsoft Research (All Phenotype And Literature Tracks)
web ucsc
updated 3 months ago by 39k • written 9.4 years ago by 154k
3
votes
0
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2.9k
views
News: Statistics and R for the Life Sciences from Harvard University (Start: 19 Jan 2015)
edX statistics
updated 14 months ago by 39k • written 8.4 years ago by ★ 2.2k
5
votes
0
replies
2.9k
views
News: Penn State now offers an Online Graduate Certificate: Applied Bioinformatics
bioinformatics-education
updated 12 weeks ago by 39k • written 8.8 years ago by 98k
0
votes
0
replies
2.9k
views
News: Travel and accommodation bursaries for workshops on Gene expression analysis, Metabolomics, RAD analysis or Population genomics in Environmental ‘Omi…
workshop
updated 18 months ago by 39k • written 8.9 years ago by ★ 3.9k
3
votes
2
replies
2.9k
views
News: Bioinformatics On Windows And Windows Cloud
windows cloud
updated 3 months ago by 39k • written 10.5 years ago by ▴ 20
4
votes
2
replies
2.9k
views
News: NCBI NOW (Next generation sequencing Online Workshop) October 13 - 23 , 2015
NCBI DNA-Seq NGS RNA-Seq
updated 9 weeks ago by 39k • written 7.7 years ago by ★ 2.2k
3
votes
0
replies
2.9k
views
News: Introduction to Python for Biologists and Advanced Python for Biologists courses
Python
updated 4 months ago by 39k • written 8.0 years ago by ★ 3.7k
0
votes
1
reply
2.8k
views
News: Workshop: 16S rRNA gene Metabarcoding (Berlin. 3-7 April 2017)
next-gen alignment blast R
updated 6 weeks ago by 39k • written 6.3 years ago by ★ 2.3k
0
votes
0
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2.8k
views
News: Bioinformatics Hands-On Workshop: Discovering standard and non-standard RNA transcripts
workshop transcripts fusion-transcripts RNA-Seq
updated 18 months ago by 39k • written 8.8 years ago by 9.9k
4
votes
0
replies
2.8k
views
News: New simulation dataset for 'A benchmark for RNA-seq quantification pipelines'
RNA-Seq
updated 8 weeks ago by 39k • written 7.0 years ago by ★ 2.5k
0
votes
0
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2.8k
views
News: WORKSHOP: Computational Approaches to Study Biological Mechanisms. Bringing together large scale ‘omics approaches and classical computational modell…
workshop
updated 18 months ago by 39k • written 8.9 years ago by ★ 3.9k
2
votes
0
replies
2.8k
views
News: New article on TCGA data & useful resource: Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers
RNA-Seq long-noncoding-RNAs
updated 9 months ago by 39k • written 7.6 years ago by 7.5k
9
votes
5
replies
2.8k
views
News: The NIH Software Discovery Index | We invite your comments
NIH software-catalog
updated 16 months ago by 39k • written 8.7 years ago by 26k
10
votes
0
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2.8k
views
News: Cfp: Camda 2013 Challenge: Big Data In Life Sciences
ngs conference
updated 3 months ago by 39k • written 10.2 years ago by ▴ 240
2
votes
3
replies
2.8k
views
News: Summer Course On Analyzing Next-Generation Sequencing Data, June 10-20, Kellog Biological Station, Michigan State University
education
updated 3 months ago by 39k • written 10.3 years ago by 98k
4
votes
0
replies
2.7k
views
News: Wed 9/25 On-Line, Live Tutorial For Integrated Genome Browser
visualization ChIP-seq RNA-seq igv genome-browser
updated 3 months ago by 39k • written 9.7 years ago by ★ 2.3k
13
votes
2
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2.7k
views
News: A Summary Of All Encode Related News On The Openhelix Blog: Encode Floods The News
encode
updated 3 months ago by 39k • written 10.7 years ago by 98k
7
votes
0
replies
2.7k
views
News: Correction for "A benchmark for RNA-seq quantification pipelines"
RNA-seq
updated 8 weeks ago by 39k • written 7.0 years ago by ▴ 70
22
votes
3
replies
2.7k
views
News: Biostar: 10,000 Question Milestone
meta
updated 3 months ago by 39k • written 10.0 years ago by 98k
3
votes
0
replies
2.7k
views
News: DNA Variant Calling Workshop
next-gen SNP
updated 8 weeks ago by 39k • written 7.0 years ago by ▴ 460
4
votes
3
replies
2.7k
views
News: -max_target_seqs 1 in NCBI standalone BLAST does not do what you think it does
blast
updated 7 days ago by 39k • written 4.6 years ago by 11k
5
votes
1
reply
2.7k
views
News: Canadian Bioinformatics Workshops Series Announced For 2014
training
updated 3 months ago by 39k • written 9.5 years ago by 20k
10
votes
17
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2.7k
views
7 follow
News: Tell us what you think of the ENA browser?
ena
updated 7 weeks ago by 39k • written 6.5 years ago by ★ 1.8k
0
votes
0
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2.7k
views
News: LAST CALL: Hands-On NGS Data Analysis Workshops 2014
NGS microRNA workshop RNA-Seq
updated 12 weeks ago by 39k • written 8.9 years ago by 9.9k
4
votes
4
replies
2.7k
views
News: Join The Dnanexus Developer Program
api cloud
updated 3 months ago by 39k • written 10.0 years ago by ▴ 30
4
votes
0
replies
2.7k
views
News: Python for Scientists - FREE Ebook from O'Reilly
python Data-Analysis
updated 9 weeks ago by 39k • written 7.7 years ago by ★ 2.2k
6
votes
1
reply
2.7k
views
News: GMOD Online Training 2014 coming up
galaxy chado gmod annotation
updated 12 weeks ago by 39k • written 9.1 years ago by 11k
1
vote
0
replies
2.6k
views
News: Workshop: Oxford Nanopore MinION Sequencing - Data Handling, Analysis and Applications, 1 November 2016, Edinburgh
Oxford-Nanopore training minION
updated 7 weeks ago by 39k • written 6.7 years ago by ★ 3.7k
0
votes
0
replies
2.6k
views
News: Workshops in Bioinformatics in 2019
assembly R RNA-Seq Python
updated 6 days ago by 39k • written 4.4 years ago by ★ 2.3k
2
votes
0
replies
2.6k
views
News: WORKSHOP - Introduction to Python for biologists
next-gen python SNP RNA-Seq
updated 6 weeks ago by 39k • written 6.2 years ago by ▴ 110
11
votes
1
reply
2.6k
views
News: NGS Data Analysis Workshop for Beginners in Munich (full)
RNA-Seq training NGS workshop
updated 10 months ago by 39k • written 6.8 years ago by 9.9k
6
votes
1
reply
2.6k
views
News: "Oxford University Press to Publish NAR Genomics and Bioinformatics"
journal
updated 2 days ago by 39k • written 4.1 years ago by 154k
8
votes
0
replies
2.6k
views
News: Plos Computational Biology: Translational Bioinformatics
publications plos
updated 3 months ago by 39k • written 10.2 years ago by 9.6k
0
votes
3
replies
2.6k
views
News: Physalia-courses: 16S rRNA gene Metabarcoding Workshop
RNA-seq sequencing SNP gene sequence
updated 7 weeks ago by 39k • written 6.6 years ago by ★ 2.3k
0
votes
0
replies
2.6k
views
News: course: Advanced R Programming. Berlin
R
updated 14 days ago by 39k • written 5.4 years ago by ★ 2.3k
2
votes
0
replies
2.6k
views
News: 2nd Edition of the Biostar Handbook. New online course starts now.
biostar-handbook
updated 6 days ago by 39k • written 4.4 years ago by 98k
0
votes
0
replies
2.6k
views
News: Call-for-Papers in Epigenomics (BMRI, impact factor 2.7)
epigenomics papers
updated 12 weeks ago by 39k • written 8.6 years ago by • 0
3
votes
0
replies
2.6k
views
News: SeqAhead - COST - Bioinformatics for Non-Coding RNAs: State-of-the-art Training Workshop: 30/6-3/7/2014, Athens, Greece
RNA-Seq workshop lncRNA microRNA
updated 12 weeks ago by 39k • written 9.0 years ago by ★ 1.3k
1
vote
0
replies
2.5k
views
News: Bioconductor/R Workshop For High-Throughput Data Analysis (Web Version)
microarray bioconductor online next-gen
updated 3 months ago by 39k • written 9.7 years ago by ▴ 10
11
votes
13
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2.5k
views
News: Ensembl datacentre shut-down: Friday 26th August - Tuesday 30th August 2016
Maintenance Ensembl
updated 7 weeks ago by 39k • written 6.8 years ago by ★ 2.2k
1,000 results • Page 3 of 20
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Comment: RNASeq gene labeling and mRNA filter from bulkRNA data. by ATpoint 72k
This information is annotated in GTF files. You can get them for almost every annotated species from Ensembl. There is a column `gene_bioty…
Answer: DE genes across multiple scRNAseq clusters-are they significantly enriched? by ATpoint 72k
First of all, with thousands of DEGs you might want to choose a DE framework that allows testing against a fold change threshold, such as `…
Comment: PacBio Pipeline and Tools for Variant Call by Kiran ▴ 80
Thanks a lot William, I am Clear now
Comment: The famous WGS dataset, Ashkenazi Trio? by cmdcolin ★ 3.0k
what is valuable information to you
Answer: Why weblogo of biopython doesn't work? by minakshiboruahassam • 0
The weblogo3 application is giving same file even if u run the scripts separately on python standalone or whatever. The weblogo command is …
Answer: Make a BedGraph file by rfran010 ▴ 80
I would suggest bedtools makewindows to generate your 3,000bp bins then bedtools coverage to generate fraction of repeats over your windows…
Answer: What is the best way to clean bulk RNA-seq data? by rfran010 ▴ 80
Honestly, I am a fan of visualizing to select a threshold since these can depend on the specific experiment. I would even just run standard…
Answer: Help with running ATAC using Encode pipeline by rfran010 ▴ 80
Read all instructions carefully Specifically, this info is under the "Input JSON file specification" section with details in the followin…
Answer: BioInformatics, Software by rfran010 ▴ 80
There have been some good suggestions, but it seems like you may be asking one of two questions, either (1) how to do bioinformatics? or (2…
Answer: Genome assembly statistical tools by Bryan • 0
I'll follow up what a few others have mentioned, but I like stats.sh within the BBTools package for raw assembly stats. I'll then polish my…
Comment: how to design a guide RNA by rfran010 ▴ 80
I agree this is very basic CRISPR mechanism and you'd be better off reading sites that could explain better than me. However, there is a lo…
Comment: ATAC peak-calling: same peak ID across multiple experimental conditions? by rfran010 ▴ 80
You want to use the MACS2 score columns? You can retain these with bedtools option `-c` . This will retain the score columns from any merge…
Comment: best annotation approach for peaks by rfran010 ▴ 80
The number of regions annotated as "Promoters" is the same regardless of TSS length? You can add this argument to annotatePeak (for mouse M…
Answer: Optimum setting for local blastp for ~10K sequences by GenoMax 129k
It is possible that NCBI keeps the entire `nr` indexes in memory and searches against that so there is no I/O involved. NCBI now also uses …
Comment: Counting intronic reads in bulk RNA-seq by swbarnes2 13k
10x does give you a big flashing warning telling you what the new default is, and tells you how to redo it without that if it's not what yo…
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