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277
votes
39
replies
168k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 10 weeks ago by 39k • written 8.8 years ago by 20k
277
votes
33
replies
94k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 3 months ago by 39k • written 9.6 years ago by 20k
238
votes
176
replies
85k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 13 days ago by 39k • written 7.8 years ago by ★ 4.6k
196
votes
44
replies
69k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 4 months ago by 39k • written 10.7 years ago by 20k
148
votes
35
replies
59k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 3 months ago by 39k • written 10.5 years ago by ★ 1.6k
146
votes
69
replies
44k
views
19 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 9 weeks ago by ▴ 10 • written 5.5 years ago by 85k
145
votes
34
replies
52k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 3 months ago by 39k • written 10.1 years ago by 5.9k
142
votes
21
replies
29k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 13 months ago by 39k • written 8.5 years ago by ★ 1.6k
136
votes
25
replies
77k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 14 months ago by 39k • written 11.1 years ago by ★ 4.2k
130
votes
123
replies
30k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 11 weeks ago by ★ 1.1k • written 4.6 years ago by 85k
116
votes
66
replies
41k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 12 weeks ago by 39k • written 4.9 years ago by 72k
101
votes
6
replies
23k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 12 weeks ago by 39k • written 4.8 years ago by 16k
99
votes
8
replies
27k
views
8 follow
Tutorial: Guide to TCGA data
cancer RNA-Seq clinical TCGA
updated 9 weeks ago by 39k • written 7.3 years ago by ★ 1.1k
99
votes
16
replies
30k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 12 weeks ago by 39k • written 6.8 years ago by 26k
94
votes
25
replies
31k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 3 months ago by 39k • written 10.7 years ago by 98k
92
votes
105
replies
36k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 12 weeks ago by 39k • written 4.8 years ago by 85k
89
votes
19
replies
31k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray bioconductor expression classification
updated 3 months ago by 39k • written 9.6 years ago by 20k
83
votes
34
replies
16k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 11 days ago by • 0 • written 5.0 years ago by ★ 1.3k
83
votes
21
replies
16k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 12 weeks ago by 39k • written 2.6 years ago by 2.9k
82
votes
28
replies
28k
views
19 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 3 months ago by 39k • written 7.2 years ago by 20k
82
votes
21
replies
74k
views
13 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 3 months ago by ★ 3.0k • written 4.9 years ago by ▴ 540
81
votes
8
replies
8.0k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop lectures genomics training
updated 3 months ago by 39k • written 9.0 years ago by 19k
80
votes
2
replies
54k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 3 months ago by 39k • written 9.9 years ago by 11k
78
votes
42
replies
29k
views
25 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 29 days ago by 39k • written 9.6 years ago by ★ 7.7k
76
votes
70
replies
16k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 12 weeks ago by 39k • written 5.3 years ago by 85k
76
votes
13
replies
14k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 20 months ago by 39k • written 9.0 years ago by 19k
74
votes
13
replies
66k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r cancer classification
updated 7 months ago by 39k • written 9.5 years ago by ★ 1.2k
73
votes
14
replies
14k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 3 months ago by 39k • written 10.0 years ago by 9.6k
72
votes
60
replies
24k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 3 months ago by 39k • written 5.7 years ago by 85k
72
votes
48
replies
16k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs alignment bwa
updated 3 months ago by 39k • written 10.3 years ago by 33k
71
votes
3
replies
35k
views
Tutorial: Revisiting the FastQC read duplication report
fastqc
updated 18 months ago by 39k • written 8.9 years ago by 98k
70
votes
26
replies
25k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 3 months ago by 39k • written 9.3 years ago by 98k
70
votes
5
replies
10k
views
8 follow
Tutorial: Bioinformatics For Metagenomic Analyses
QC taxonomy metagenomics
updated 14 months ago by 39k • written 9.2 years ago by ★ 1.8k
67
votes
6
replies
25k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 3 months ago by 39k • written 10.8 years ago by 98k
65
votes
26
replies
12k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 12 weeks ago by 39k • written 4.3 years ago by 16k
65
votes
9
replies
48k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 4 months ago by 39k • written 9.9 years ago by ★ 3.0k
64
votes
26
replies
12k
views
7 follow
Tutorial: Parallel processing in R
biocparallel mclapply foreach R
updated 12 weeks ago by 39k • written 5.7 years ago by 85k
64
votes
5
replies
6.8k
views
10 follow
Tutorial: Informatics of RNA-Seq.
next-gen RNA-Seq
updated 7 months ago by 39k • written 7.8 years ago by 12k
63
votes
13
replies
12k
views
11 follow
Tutorial: Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.
muTect GATK Picard Exome
updated 16 months ago by 39k • written 8.6 years ago by ★ 2.3k
60
votes
52
replies
40k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 12 weeks ago by 39k • written 6.7 years ago by ★ 3.3k
60
votes
6
replies
9.0k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 3 months ago by 39k • written 9.8 years ago by 9.6k
60
votes
2
replies
7.0k
views
Tutorial: Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 3 months ago by 39k • written 10.8 years ago by 98k
59
votes
43
replies
19k
views
18 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign pacbio arrow smrt-limk
updated 12 weeks ago by 39k • written 5.7 years ago by ★ 1.4k
59
votes
15
replies
12k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 12 days ago by 39k • written 4.7 years ago by 16k
58
votes
25
replies
37k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 11 weeks ago by 39k • written 6.9 years ago by ★ 9.3k
53
votes
5
replies
14k
views
6 follow
Tutorial: Machine Learning For Cancer Classification - Part 4 - Plotting A Kaplan-Meier Curve For Survival Analysis
r
updated 8 months ago by 39k • written 9.5 years ago by ★ 1.2k
51
votes
19
replies
42k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization bigwig chip-seq rna-seq
updated 3 months ago by 39k • written 11.1 years ago by 11k
51
votes
3
replies
22k
views
Tutorial: Sam File Format - Lesser Known Tips And Tricks
sam
updated 3 months ago by 39k • written 10.4 years ago by ▴ 300
50
votes
3
replies
4.2k
views
Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 12 weeks ago by 39k • written 4.4 years ago by 72k
49
votes
1
reply
6.6k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 3 months ago by 39k • written 2.7 years ago by 72k
358 results • Page 1 of 8
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ChatGPT optimized for bioinformatics questions
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Comment: ChatGPT optimized for bioinformatics questions
ChatGPT optimized for bioinformatics questions
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ChatGPT optimized for bioinformatics questions
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Recent Replies
Comment: retaining only the clusters of interest by Ram 39k
You're close. The `subset` function serves a similar functionality as the base, but since the Seurat object is an S3 object, it subsets bas…
Answer: ChatGPT optimized for bioinformatics questions by Ram 39k
I asked the same questions to tinyBio and chatGPT and chatGPT gave me better answers. This could be because chatGPT has been out for a whil…
Comment: ChatGPT optimized for bioinformatics questions by Sasha ▴ 240
Hi GenoMax - it's primed on Github repos, some personality tuning, and some prompt assumptions based on the context of the site being bioin…
Answer: Diff Bind Questions by Rory Stark ★ 1.7k
The `DiffBind` vignette attempts to explain how tis in handled in step-by-step detail, that is another good place to start. The direct a…
Answer: CHiP-Seq Questions by Rory Stark ★ 1.7k
You may want to add `Replicate` to your design formula to model the batch effect (assuming the same replicate is the outlier in both condit…
Comment: ChatGPT optimized for bioinformatics questions by GenoMax 129k
Can you elaborate on how you trained the bot specifically on bioinformatics content? Where is the content coming from?
Comment: Visualizing several genomes/plasmids in a single figure by GenoMax 129k
As a test I posed your question to a bioinformatics bot that was just announced on Biostars. You can find it here : https://ai.tinybio.clou…
Comment: Which method is the best for using in "dba.count" in Diffbind R package by Rory Stark ★ 1.7k
If you are calling `dba.normalize()` directly, it must be called *after* calling `dba.count()`. `dba.count()` will apply the default normal…
Comment: switching from illumination to NEB prep kits by GenoMax 129k
If you are simply replacing the library prep kit then it will be compatible with normal illumina libraries. If there is a different adapter…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu by Zhichao • 0
yes, I have activated this conda environment. And the conda is in `PATH` . At first, I create a new conda environment `conda create -n ne…
Comment: Limma returned only positive logFC values by ATpoint 72k
Raw counts, raw meaning not manipulated by any transformation. See limma and edgeR manual, it clearly covers that for using limma-trend and…
Comment: Alternative To interactions comparison in limma in DESeq2 by ATpoint 72k
https://support.bioconductor.org/p/9143932/ -- see the lower parts where Michael Love answers, it comes down to numeric contrasts.
Comment: Limma returned only positive logFC values by melissachua90 ▴ 40
The `mat` is log2-normalized raw data. Is it feasible? Or should I feed in counts?
Comment: DESeq2 for different design and normalized counts by ATpoint 72k
Nope, please read the manual of DESeq2, it clearly tells to use raw counts. What "normalized counts" do you have exactly? limma-trend might…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu by ATpoint 72k
Did you activate your conda environment? Is conda in `PATH`? Please describe what you did.
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