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Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 3 days ago by ★ 1.1k • written 4.4 years ago by 84k
276
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39
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164k
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29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 14 hours ago by 38k • written 8.6 years ago by 20k
12
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4
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1.8k
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Tutorial: Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR DESeq2
updated 1 day ago by 38k • written 5.5 years ago by ▴ 570
5
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1.7k
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Tutorial: A Guide to DNA Sequencing Techniques Part 1
dna sanger sequencing pyrosequencing
updated 14 hours ago by 38k • written 7.7 years ago by ▴ 370
0
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0
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2.0k
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Tutorial: Protein expression analysis
protein-analysis
updated 4 days ago by 38k • written 8.0 years ago by • 0
1
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0
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152
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Tutorial: ChIP-Seq Analysis Tutorial
Epigenetics Bowtie2 MACS2 ChIP-Seq Motif
updated 2 days ago by 70k • written 2 days ago by ▴ 20
1
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0
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1.9k
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Tutorial: A short primer to pairwise alignment
pairwise-alignment blastp pam blosum
updated 14 hours ago by 38k • written 7.7 years ago by ▴ 370
7 results • Page 1 of 1
Recent Votes
Difference between RNA-sq and Transcriptome
Rat lung transcriptome
A: microarray, RNAseq, CEL, edgeR, etc. for DGE analysis
Converting SNP from chr:pos to rs number using PLINK?
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
Answer: Cellranger sequencing
Answer: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ?
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Recent Replies
Comment: Remove part of headers in FASTA file by Pierre Lindenbaum 153k
Use `cut -d ' '`
Answer: Problem running interproscan-5.15-54.0 for protein sequences by Pratyay • 0
Hi, can you guide me how to compile the src folder? Many thanks!
Comment: Matching gene-expression data with clinical data: best practices. by krushnach80 ★ 1.1k
You can check [this][1] [1]: https://www.linkedomics.org/
Answer: Matching gene-expression data with clinical data: best practices. by jose.sgomez94 • 0
Figured out one can use the TCGAutils package in R and UUIDtobarcode() function. Still, suggestions of best practices would be awesome!
Answer: Understanding multifactor designs and control variables in DESeq2 by FrankStarling ▴ 50
https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2021/RNAseq/Markdowns/10_DE_analysis_with_DESeq2.Solutions.html …
Comment: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ? by Adaline.D • 0
I appreciate your help, LChart! I will use raw data in case of a substantial loss of power. (1) The publication did a PCA and then analy…
Answer: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ? by LChart 2.2k
Short answer: use LIMMA Long answer: edgeR uses a negative binomial model, and expects *counts* and not *values*. Please read section 2.8.…
Comment: Python formatting when visualizing Primer3-py dimers by bhumm ▴ 30
Wayne, both of these methods work beautifully. I really appreciate the detail you provided, thank you so much for your help!
Comment: Ortholog assembly and extraction by dthorbur ▴ 420
I really like `orthofinder` and use it frequently, but there are also plenty of other tools out there. [Here](https://academic.oup.com/mbe/…
Comment: chloroplast genome gaps by ugur • 0
after alignment, it occurs in different sizes of gaps
Answer: Cellranger sequencing by ATpoint 70k
Not that I am aware of. Unlike methods such as salmon it does genome alignment and does not resolve the exact transcript expression composi…
Answer: Assembly at lineage level from shotgun data ? by Mensur Dlakic ★ 23k
The paper I list below is meant for improving the existing MAG assemblies. Yet the program will do what you want: if you give it a referenc…
Comment: Ortholog assembly and extraction by GenoMax 127k
Many seem to use `orthofinder` for this purpose. See if it is useful: https://github.com/davidemms/OrthoFinder
Answer: Python formatting when visualizing Primer3-py dimers by Wayne ★ 1.7k
Try this so you'll see that using [tabulate](https://github.com/astanin/python-tabulate) to print the dataframe causes it to respect the li…
Comment: Python formatting when visualizing Primer3-py dimers by bhumm ▴ 30
Glad I am making this more clear. The 'test1' in practice will be the 'primer name' to allow for tracking of other metrics (Tm, hairpin str…
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