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training handbook

updated 7 weeks ago by Biostar 2.3k • written 7.0 years ago by Istvan Albert 99k

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meta biostars

updated 4 weeks ago by Ram 41k • written 11.0 years ago by Istvan Albert 99k

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biostars

updated 9 months ago by Ram 41k • written 10.9 years ago by Istvan Albert 99k

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publication NGS

updated 7 months ago by Ram 41k • written 6.9 years ago by David Langenberger 10k

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windows

updated 7 months ago by Ram 41k • written 7.7 years ago by poisonAlien ★ 3.2k

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meta biostars

updated 9 months ago by Ram 41k • written 8.7 years ago by Istvan Albert 99k

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genome deep-learning google

updated 6 months ago by Ram 41k • written 6.0 years ago by Hussain Ather ▴ 990

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gamestorming

updated 9 months ago by Ram 41k • written 11.2 years ago by Giovanni M Dall'Olio 28k

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DNAseq DNA WGS

updated 5 months ago by Alex Reynolds 35k • written 5 months ago by David Langenberger 10k

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Transcriptomics DNA-Seq Variant-Calling RNA-Seq

4 months ago by David Langenberger 10k

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Epigenetics Workshop Bisulfite-Sequencing

updated 7 months ago by Ram 41k • written 7.5 years ago by Adele Feuerstein ▴ 460

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education

updated 9 months ago by Ram 41k • written 11.2 years ago by phcompeau ▴ 330

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ncbi genbank pubmed command-line entrez

updated 9 months ago by Ram 41k • written 9.8 years ago by Pierre Lindenbaum 158k

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biostars

updated 9 months ago by Ram 41k • written 10.8 years ago by Istvan Albert 99k

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ncbi pubmed

updated 9 months ago by Ram 41k • written 10.1 years ago by Pierre Lindenbaum 158k

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crowd-coding

updated 9 months ago by Ram 41k • written 10.4 years ago by Pierre Lindenbaum 158k

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6.9k

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blast alignment

updated 6 months ago by Ram 41k • written 5.2 years ago by Farbod ★ 3.4k

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github git

updated 8 months ago by Ram 41k • written 9.5 years ago by Pierre Lindenbaum 158k

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2.9k

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Popular Question to doggie • 0

Recent Replies

Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT by tw_140 • 0

Thank you for the suggestions! I checked some housekeeping genes and they are represented in the dataset for all samples (albeit, some at …

Answer: Moving AF tag to new column in a VCF file by Pierre Lindenbaum 158k

extract the vcf as a tab delimited file, something like (not tested) bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%FORMAT/AF]\n' in…

Comment: How can I map coordinates between two strains of yeast? by GenoMax 136k

> genome sequences of two different strains of yeast Are they the same species?

Comment: How to do simple pathway analysis? by he1k • 0

Hi [AK][1], I downloaded the KO.keg file. I was wondering what tool(s) you used to generate the "KO.tsv" file as you showed here. Thanks. …

Comment: How can I map coordinates between two strains of yeast? by dthorbur ▴ 840

I think that is an alternative to a synteny analysis, but I only know liftover in terms of annotations. OP asks for "coordinates between th…

Comment: Bowtie mapping for single_end read by ATpoint 78k

I am sceptical any tweaking of parameters will make a notable difference. Parameters in bowtie are very good at default, and given it's ChI…

Comment: How can I map coordinates between two strains of yeast? by cmdcolin ★ 3.4k

would something like liftover not be recommended? honest question

Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT by dthorbur ▴ 840

That's good. But I still suspect this data might be really difficult to analyse. I have a handful of suggestions I would do to assess wheth…

Comment: Identify clusters of populations based on gene expression by dthorbur ▴ 840

One gene might not be enough data to "cluster" based on expression. Unless I'm missing something, that would just be breaking a single cont…

Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT by tw_140 • 0

Yes, I performed ribosome depletion using an RNAse H based method.

Comment: Circular genome browser by cmdcolin ★ 3.4k

that's great to hear. one "proxy" for interactive is looking at the JS based tools, many are web based and interactive as a result. I have …

Comment: R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales by TC_Chang ▴ 10

Hi jv, Thank you for your reply. Basically, I'm trying to generate the figure shown below with two different y-axis scales. Any suggestio…

Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT by dthorbur ▴ 840

I don't have a suggestion for low yield DE analyses, but I am curious about the samples. Did you conduct any ribo-depletion steps prior to …

Answer: How can I map coordinates between two strains of yeast? by dthorbur ▴ 840

It sounds like you are looking for synteny between the two genomes. I'm assuming they are assembled, but that may not be the case. If so, […

Comment: Identify clusters of populations based on gene expression by Nitin Narwade ★ 1.5k

Why don't you just plot it on your UMAP If it is specific to one cluster/sub-population you should get a relatively high expression in that…

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