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Tutorial: GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo R data-mining Gene-pathway-enrichment RNA-Seq
updated 5 months ago by 41k • written 11 months ago by ▴ 360
1
vote
0
replies
2.3k
views
Tutorial: GEO Data Mining (II) - Differential gene expression analysis and visualization with complete code sharing
geo R data-mining differential-gene-expression RNA-Seq
updated 5 months ago by 41k • written 11 months ago by ▴ 360
5
votes
0
replies
1.2k
views
Tutorial: GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo RNA-Seq data-mining SRA
updated 5 months ago by 41k • written 11 months ago by ▴ 360
6
votes
0
replies
3.3k
views
Tutorial: How to download GEO data Quickly and easily
geo RNA-Seq R data-mining
9 months ago by Novogene ▴ 360
50
votes
1
reply
7.9k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 9 months ago by 41k • written 3.2 years ago by 78k
1
vote
3
replies
788
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbssampling splice
8 months ago by barslmn ★ 2.0k
73
votes
60
replies
26k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 9 months ago by 41k • written 6.2 years ago by 86k
14
votes
31
replies
6.1k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 8 months ago by 41k • written 4.3 years ago by 8.4k
1
vote
2
replies
1.3k
views
Tutorial: ViennaRNA package installation in Windows
windows rna mfold viennarna
updated 5 months ago by 41k • written 14 months ago by ▴ 20
132
votes
123
replies
34k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 8 months ago by ★ 1.1k • written 5.1 years ago by 86k
11
votes
7
replies
9.9k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 6 months ago by 41k • written 2.7 years ago by ▴ 360
84
votes
21
replies
20k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 8 months ago by 41k • written 3.1 years ago by 3.1k
83
votes
34
replies
17k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 6 months ago by • 0 • written 5.4 years ago by ★ 1.3k
85
votes
2
replies
57k
views
6 follow
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 9 months ago by 41k • written 10.4 years ago by 11k
15
votes
5
replies
12k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 8 months ago by 41k • written 6.0 years ago by ▴ 770
39
votes
8
replies
12k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 8 months ago by 41k • written 3.2 years ago by 3.1k
75
votes
14
replies
15k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 9 months ago by 41k • written 10.5 years ago by 9.7k
4
votes
13
replies
12k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 5 months ago by 41k • written 4.8 years ago by ▴ 140
12
votes
4
replies
5.1k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 9 months ago by 41k • written 2.8 years ago by ▴ 130
29
votes
10
replies
73k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 8 months ago by 41k • written 2.7 years ago by ★ 1.5k
148
votes
70
replies
48k
views
20 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 3 months ago by ▴ 260 • written 6.0 years ago by 86k
196
votes
44
replies
70k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 10 months ago by 41k • written 11.2 years ago by 20k
45
votes
2
replies
36k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 9 months ago by 41k • written 11.7 years ago by ▴ 540
95
votes
105
replies
41k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 8 months ago by 41k • written 5.3 years ago by 86k
117
votes
66
replies
44k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 8 months ago by 41k • written 5.4 years ago by 78k
65
votes
26
replies
13k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 8 months ago by 41k • written 4.7 years ago by 16k
12
votes
20
replies
13k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 8 months ago by 41k • written 4.5 years ago by ★ 16k
4
votes
2
replies
2.3k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0 beagle
updated 8 months ago by 41k • written 4.5 years ago by ★ 9.3k
51
votes
14
replies
79k
views
10 follow
Tutorial: Using R in Conda
R
updated 8 months ago by 41k • written 3.4 years ago by ▴ 780
99
votes
16
replies
32k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 8 months ago by 41k • written 7.3 years ago by 26k
31
votes
6
replies
11k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 8 months ago by 41k • written 3.5 years ago by 86k
238
votes
176
replies
90k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 6 months ago by 41k • written 8.3 years ago by ★ 4.7k
8
votes
1
reply
1.3k
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
fasta awk
updated 8 months ago by 41k • written 2.7 years ago by 86k
21
votes
10
replies
6.3k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 8 months ago by 41k • written 3.2 years ago by 12k
12
votes
2
replies
1.2k
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R
updated 8 months ago by 41k • written 2.7 years ago by 12k
149
votes
35
replies
61k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 9 months ago by 41k • written 11.0 years ago by ★ 1.6k
15
votes
2
replies
3.6k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 8 months ago by 41k • written 3.2 years ago by 3.1k
16
votes
7
replies
15k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 8 months ago by 41k • written 4.5 years ago by ▴ 310
288
votes
33
replies
102k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 9 months ago by 41k • written 10.1 years ago by 20k
5
votes
1
reply
4.2k
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
updated 5 minutes ago by • 0 • written 2.9 years ago by 136k
11
votes
0
replies
6.1k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
updated 8 months ago by 41k • written 2.9 years ago by 136k
10
votes
0
replies
4.2k
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap
updated 8 months ago by 41k • written 2.9 years ago by 136k
11
votes
1
reply
2.5k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 8 months ago by 41k • written 2.9 years ago by ★ 25k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 8 months ago by 41k • written 9.6 years ago by ★ 1.9k
0
votes
1
reply
2.8k
views
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
biosql python taxonomy
updated 8 months ago by 41k • written 5.3 years ago by ▴ 320
6
votes
10
replies
5.0k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 8 months ago by 41k • written 5.8 years ago by ▴ 370
43
votes
6
replies
12k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 9 months ago by 41k • written 9.8 years ago by 6.0k
5
votes
3
replies
5.1k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 8 months ago by • 0 • written 6.1 years ago by ▴ 130
16
votes
11
replies
7.9k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
8 months ago by Ram 41k
104
votes
6
replies
24k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 8 months ago by 41k • written 5.2 years ago by 16k
318 results • Page 2 of 7
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Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
Answer: 1000 genomes project reference panel - GRCh38
Answer: 1000 genomes project reference panel - GRCh38
Comment: IMPUTE2- Map file for custom reference panel
IMPUTE2- Map file for custom reference panel
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Comment: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates with by jucosie • 0
Hello, I am reviewing some old scripts in which I used clumpify.sh (BBMap 38.90) with the following parameters: ./clumpify.sh in1=$dir_c…
Comment: Problematic fastq files...How can we trust them? by Istvan Albert 99k
perhaps ask her about the origin of the data, how was the data postprocessed FASTQ data is a bit more resilient than other types of data a…
Answer: GO categorization by Istvan Albert 99k
If you have an organism that lacks the GO to gene mapping then you have to find a way to assign these terms to your genes. Basically your …
Comment: doubt about usage of megahit by Istvan Albert 99k
you have not mentioned what kind of resources you have, how much data you have to process and what the expected genome/transcriptome sizes …
Comment: Problematic fastq files...How can we trust them? by ATpoint 78k
Then tell her to bring proper data. In the lab you also don't use buffers with mold growing in it, and in bioinformatics we don't start wit…
Comment: Problematic fastq files...How can we trust them? by blackadder ▴ 30
Its not my data. An external researcher is visiting and she wanted from us to do some bioinformatics... The samples were not sequenced by u…
Comment: Tools or R / Python packages to perfom ML models by sil_bioinfo ▴ 30
Oh, I understand. Thank you so much for your help! The truth is that there is so much information, so many packages, libraries, tutorials,…
Comment: Tools or R / Python packages to perfom ML models by Matthias Zepper 4.2k
Just to clarify: Many ML models are trained and executed using dedicated software libraries for machine learning and artificial intellige…
Answer: Problematic fastq files...How can we trust them? by ATpoint 78k
> I assume that maybe all these are fixable with a script but my question is, can we trust these files? Is it worth spending time and effor…
Comment: Tools or R / Python packages to perfom ML models by sil_bioinfo ▴ 30
My main idea is to be able to classify patients with active TB, LTBI and healthy patients as well as possible. The problem is that within t…
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by rpolicastro 12k
They could have saved themselves a ton of money by sequencing this on a miseq.
Comment: Annotate Unplaced Scaffold with Chromosome Information by cmdcolin ★ 3.4k
I think there are tools like ragtag https://github.com/malonge/RagTag that could help. you can also align your reads back to your new assem…
Comment: An incomprehensible error with R package gggenes by ATpoint 78k
It's not stupid, just a bit lazy ;-)
Comment: Adding functional annotation and meta-data of MAKER/BRAKER GFF by ben@f • 0
Hi, did you find an effective solution for this problem? beside Agat and
Comment: An incomprehensible error with R package gggenes by alice005201314 • 0
Thank you. I asked a stupid question.
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