Bioinformatics Answers

3,465 results • Page 1 of 70

730

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161

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108k

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100 follow

training handbook

updated 10 days ago by Biostar 1.6k • written 6.3 years ago by Istvan Albert 97k

130

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123

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28k

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23 follow

cox gene-expression survival-analysis geo

updated 2 days ago by krushnach80 ★ 1.1k • written 4.4 years ago by Kevin Blighe 84k

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105

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34k

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25 follow

1000genomes PLINK PCA

updated 11 days ago by Ram 38k • written 4.6 years ago by Kevin Blighe 84k

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16k

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enrichment david

updated 10 days ago by Ram 38k • written 5.1 years ago by Kevin Blighe 84k

144

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43k

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microarray RNA-Seq R network

updated 11 days ago by Ram 38k • written 5.3 years ago by Kevin Blighe 84k

116

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40k

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20 follow

aspera fastq-dump Fastq ENA

updated 11 days ago by Ram 38k • written 4.7 years ago by ATpoint 70k

206

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38k

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31 follow

r statistics python biopython

updated 28 days ago by Ram 38k • written 9.8 years ago by Medhat 9.5k

118

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87k

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22 follow

bam coverage depth next-gen-sequencing

updated 6 days ago by Raag • 0 • written 8.8 years ago by kay ▴ 330

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39k

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plotly R volcano-plot

updated 10 days ago by Ram 38k • written 6.5 years ago by steve ★ 3.3k

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14k

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17 follow

personal-genomics 23andMe

updated 23 days ago by Ram 38k • written 9.3 years ago by Istvan Albert 97k

262

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20k

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37 follow

Workshop Training Courses

updated 25 days ago by Lars ▴ 970 • written 7.9 years ago by Deepak Tanwar ★ 4.2k

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15k

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ngs alignment bwa

updated 29 days ago by Ram 38k • written 10.1 years ago by lh3 33k

105

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11k

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13 follow

epigenetics

updated 24 days ago by Ram 38k • written 9.6 years ago by ugly.betty77 ★ 1.1k

102

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knowledge career

updated 25 days ago by Ram 38k • written 9.6 years ago by brentp 24k

126

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27k

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16 follow

NGS adapter RNA-Seq

updated 15 days ago by Ram 38k • written 6.5 years ago by Lars ▴ 970

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14k

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8 follow

NGS alignment genome RNA-Seq sequence

updated 15 days ago by Ram 38k • written 4.2 years ago by David Langenberger 9.9k

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18k

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pbalign pacbio arrow smrt-limk

updated 10 days ago by Ram 38k • written 5.5 years ago by Rox ★ 1.4k

136

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20k

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20 follow

meta

updated 29 days ago by Ram 38k • written 10.3 years ago by 14134125465346445 ★ 3.6k

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6 follow

geneset genome gene abinitio

updated 15 days ago by Ram 38k • written 3.6 years ago by Juke34 7.7k

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1.8k

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workflow next-gen RNA-Seq pipeline

updated 3 days ago by Ram 38k • written 2.3 years ago by mfawzy.sami ▴ 90

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4.0k

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7 follow

meta RSS

updated 29 days ago by Ram 38k • written 10.2 years ago by Madelaine Gogol 5.3k

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5.6k

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gff parse

updated 2 days ago by Juke34 7.7k • written 4.5 years ago by a.rex ▴ 350

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7.3k

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27 follow

uses-this

updated 15 days ago by Ram 38k • written 8.5 years ago by Istvan Albert 97k

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17k

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vcf snp

updated 8 hours ago by Ram 38k • written 11.3 years ago by Kevin ▴ 640

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26k

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python

updated 29 days ago by Ram 38k • written 10.3 years ago by Click downvote ▴ 720

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1.4k

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bash

updated 2 days ago by Ram 38k • written 2.9 years ago by ATCG ▴ 380

118

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22 follow

DESeq Kallisto RNASeq Salmon DESeq2

updated 14 days ago by e.r.zakiev ▴ 30 • written 7.8 years ago by mhockin ▴ 610

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11k

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11 follow

fasta consensus bam

updated 11 days ago by Ram 38k • written 4.0 years ago by finswimmer 16k

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11k

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7 follow

biocparallel mclapply foreach R

updated 10 days ago by Ram 38k • written 5.5 years ago by Kevin Blighe 84k

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7.6k

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Deseq2 macOS gff HEloci

updated 7 days ago by Ram 38k • written 4.7 years ago by jaqx008 ▴ 110

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24k

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15 follow

RNA-seq

updated 22 days ago by Ram 38k • written 9.1 years ago by Istvan Albert 97k

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7.5k

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bam samtools

updated 2 days ago by Ram 38k • written 4.7 years ago by marongiu.luigi ▴ 670

3,465 results • Page 1 of 70

Recent Votes

Answer: multiallelic variants

Comment: Python formatting when visualizing Primer3-py dimers

Answer: Python formatting when visualizing Primer3-py dimers

get organism name from fasta file header (PYTHON)

Answer: Cellranger sequencing

Answer: Using STAR for RNA seq-alignment.

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Recent Replies

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 …

Answer: 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…

Comment: Python formatting when visualizing Primer3-py dimers by Wayne ★ 1.7k

Starting to understand what you want and why. My question is now also then do you actually want the brackets? They seem to shift the rela…

Comment: Python formatting when visualizing Primer3-py dimers by bhumm ▴ 30

Hi Wayne, Thanks for the response. I have updated the code to be more representative of the toy example I have provided - apologies for an…

Comment: chloroplast genome gaps by Pierre Lindenbaum 153k

> , but the alignment results show different size gaps. what does it mean ?

Comment: lncTar by Ram 38k

I see that you added an answer to a 2 year old post. Don't do that - what you added was "I have this problem too" comment, not an answer. I…

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