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News: New NCBI Datasets APIs to Replace Old Ones
NCBI API Datasets
2 days ago by PeterC_NCBI ▴ 330
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News: LAST CALL: Online Course - A Practical Introduction to NGS Data Analysis - October 23-25, 2023
DNA-seq Workshop RNA-seq
2 days ago by David Langenberger 10k
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108
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News: RADseq data analysis course
RADseq Phylogenomics Bioinformatics Populationgenomics Stacks
3 days ago by carlopecoraro2 ★ 2.4k
0
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184
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News: EMBL-EBI virtual course | Introduction to RNA-seq and functional interpretation
RNA-seq
updated 5 days ago by 40k • written 5 days ago by • 0
1
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165
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News: Online Training - Bioinformatics Pipeline Development with Nextflow (November 15-17, 2023)
nextflow automation pipeline development
5 days ago by David Langenberger 10k
2
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1
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219
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News: Successful NCBI NIAID Codeathon on VCF Files in SARS-CoV-2 Genomics
NCBI Codeathon
updated 3 days ago by 10k • written 6 days ago by ▴ 330
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News: Workshop - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (November 8-10, 2023 in Berlin)
workshop scRNA-Seq RNA-Seq single-cell
updated 6 days ago by 40k • written 6 days ago by 10k
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156
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News: Research Breakthrough in Identifying Viral Escape Mutations for Improved Therapeutic Design
sequence-analysis sars-cov-2 spike-protein
updated 6 days ago by 40k • written 6 days ago by • 0
8 results • Page 1 of 1
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Comment: demultiplexing with guppy_basecaller and guppy_barcoder using --detect_mid_stran
A: What'S The Difference Between Cds And Orf?
What'S The Difference Between Cds And Orf?
Answer: Filtering transcription factor and HOMER and ENCODE
Answer: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore
Answer: Number of accessible regions included by DESeq2 to generate the PCA plot with th
Updated List of Unix tutorials 2023
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Answer: Have some issues in running prokka on WSL by Philipp Bayer 7.9k
It looks like the conda-installed BLAST has issues with the system's ZSTD, which is probably some WSL weirdness. You *might* be able to fix…
Comment: Network analysis with cytoscape by Chris ▴ 180
Sure, the network represents the different expressed genes in my RNA-seq. I choosed string protein query.
Comment: Network analysis with cytoscape by Yogi ▴ 40
A few questions. 1. What does the network represent? 2. Can you insert a high level picture of the network (or pictures) if you want to zo…
Answer: Chip-Seq and correlation of bam file by jared.andrews07 ★ 15k
Use [deepTools' plotCorrelation function](https://deeptools.readthedocs.io/en/develop/content/tools/plotCorrelation.html).
Answer: Transcription factor co-localization p-values by jared.andrews07 ★ 15k
[regioneR](https://bioconductor.org/packages/release/bioc/html/regioneR.html) seems to be what you want.
Comment: Complex multifactorial DE analysis with limma/edgeR based on rnaseq data by LChart 3.4k
> Our major biological questions are: to have a general comparison of cancer vs normal “treatment” conditions; In addition if doable, to co…
Comment: Which function is best for pathway analysis? by Chris ▴ 180
Thanks @luffy! Great material but seem they didn't mention how to customize the background genes depend on our data.
Comment: CollectRnaSeqMetrics (Picard) output to convert FeatureCounts into TPM by camillab. ▴ 140
I have calculate from this [tutorial][1]. so basically it retrieve the normalized counts matrix using `Deseq2` . Do you think it is correct…
Comment: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore by GenoMax 134k
`dorado` can't demultiplex data as yet (v.0.3.4). Also no adapter trimming. So something to keep in mind if you are switching. To address …
Comment: Frustrated with DEA results by dsull ★ 4.7k
Let the data speak. If there's no difference, then there's no difference. Human clinical data is always messy and unpredictable, especiall…
Comment: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore by Ram 40k
I don't think they bought the Mac Studio just for the MiniON. If they did, that might be overkill. All things considered, I'd prefer an App…
Comment: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore by ATpoint 77k
Wondering why investing all that money for such an overpriced piece of hardware. You could get an equivalent Windows or Linux workstation f…
Answer: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore by Christopher ▴ 10
I'm using a Mac Studio with M1 Ultra chip to sequence with a MinION Mk1B now and it's working great! Fast basecalling and adaptive sequenci…
Comment: ncbi error report log for validate fastq issue by GenoMax 134k
You may want to use `--split-files` instead. With your `--split-spot` option looks like you end up with interleaved data files. Unless you …
Comment: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor by Ram 40k
Nope, I kinda gave up. I got to the image on what fragment size is (https://www.biostars.org/p/106291/#106344) but cannot figure out how to…
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