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2
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0
replies
192
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Tutorial: ChIP-Seq Analysis Tutorial
Epigenetics Bowtie2 MACS2 ChIP-Seq Motif
updated 7 days ago by 70k • written 7 days ago by ▴ 30
1
vote
0
replies
127
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine_learning papers scoring_function docking
13 days ago by Milad ▴ 10
10
votes
7
replies
1.1k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
5 hours ago by barslmn ★ 1.4k
2
votes
0
replies
647
views
Tutorial: How to download GEO data Quickly and easily
geo RNA-Seq R data-mining
29 days ago by Novogene ▴ 240
1
vote
3
replies
425
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbssampling splice
5 hours ago by barslmn ★ 1.4k
12
votes
31
replies
4.7k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 20 days ago by 38k • written 3.6 years ago by 7.8k
130
votes
123
replies
29k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 8 days ago by ★ 1.1k • written 4.4 years ago by 84k
82
votes
21
replies
15k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 20 days ago by 38k • written 2.5 years ago by 2.9k
83
votes
34
replies
15k
views
21 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
active-subnetwork enrichment pathway R
updated 20 days ago by 38k • written 4.8 years ago by ★ 1.3k
15
votes
5
replies
11k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 20 days ago by 38k • written 5.3 years ago by ▴ 740
37
votes
8
replies
9.3k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 20 days ago by 38k • written 2.5 years ago by 2.9k
3
votes
13
replies
9.5k
views
Tutorial: Merging multiple vcf files into Single vcf file
merge vcf bcftools
updated 20 days ago by 38k • written 4.1 years ago by ▴ 140
26
votes
10
replies
59k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 20 days ago by 38k • written 2.0 years ago by ★ 1.3k
144
votes
68
replies
43k
views
18 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 16 days ago by 38k • written 5.4 years ago by 84k
92
votes
105
replies
34k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 16 days ago by 38k • written 4.6 years ago by 84k
116
votes
66
replies
40k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 16 days ago by 38k • written 4.7 years ago by 70k
64
votes
26
replies
11k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 16 days ago by 38k • written 4.1 years ago by 16k
12
votes
20
replies
11k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 15 days ago by 38k • written 3.8 years ago by ★ 14k
4
votes
2
replies
2.0k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0 beagle
updated 15 days ago by 38k • written 3.8 years ago by ★ 9.3k
45
votes
14
replies
59k
views
10 follow
Tutorial: Using R in Conda
R
updated 15 days ago by 38k • written 2.7 years ago by ▴ 690
31
votes
9
replies
24k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 15 days ago by 38k • written 2.6 years ago by ▴ 140
99
votes
16
replies
30k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 15 days ago by 38k • written 6.7 years ago by 26k
31
votes
6
replies
8.7k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 15 days ago by 38k • written 2.9 years ago by 84k
8
votes
1
reply
1.0k
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
fasta awk
updated 15 days ago by 38k • written 2.0 years ago by 84k
20
votes
10
replies
4.7k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 15 days ago by 38k • written 2.6 years ago by 11k
12
votes
2
replies
1.0k
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R
updated 15 days ago by 38k • written 2.0 years ago by 11k
14
votes
2
replies
2.8k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 15 days ago by 38k • written 2.5 years ago by 2.9k
4
votes
0
replies
1.7k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 15 days ago by 38k • written 2.9 years ago by 70k
16
votes
7
replies
12k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 15 days ago by 38k • written 3.8 years ago by ▴ 310
275
votes
33
replies
92k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 29 days ago by 38k • written 9.4 years ago by 20k
5
votes
0
replies
3.5k
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 15 days ago by 38k • written 2.2 years ago by 127k
10
votes
0
replies
4.5k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
updated 15 days ago by 38k • written 2.2 years ago by 127k
10
votes
0
replies
2.7k
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap
updated 15 days ago by 38k • written 2.2 years ago by 127k
11
votes
1
reply
2.2k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 15 days ago by 38k • written 2.2 years ago by ★ 23k
40
votes
9
replies
10k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 23 days ago by 38k • written 9.0 years ago by ★ 1.9k
0
votes
1
reply
2.4k
views
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
biosql python taxonomy
updated 15 days ago by 38k • written 4.6 years ago by ▴ 310
6
votes
10
replies
4.3k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 15 days ago by 38k • written 5.1 years ago by ▴ 340
43
votes
6
replies
11k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 27 days ago by 38k • written 9.2 years ago by 5.9k
5
votes
3
replies
4.5k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 13 days ago by • 0 • written 5.4 years ago by ▴ 130
16
votes
11
replies
7.3k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
15 days ago by Ram 38k
42
votes
33
replies
6.8k
views
8 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
meta how-to documentation
15 days ago by Ram 38k
100
votes
6
replies
22k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 15 days ago by 38k • written 4.6 years ago by 16k
18
votes
40
replies
16k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 15 days ago by 38k • written 6.8 years ago by ▴ 170
23
votes
4
replies
6.2k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 15 days ago by 38k • written 3.6 years ago by 70k
15
votes
4
replies
4.1k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 15 days ago by 38k • written 2.7 years ago by ▴ 300
26
votes
0
replies
2.1k
views
Tutorial: Resources / databases for clinical interpretation of cancer variants
interpretation cancer annotation variant
updated 15 days ago by 38k • written 3.5 years ago by 19k
10
votes
1
reply
2.0k
views
Tutorial: introduce a tool for fast identification of SARS-CoV-2 and other microbes from sequencing data
SARS-CoV-2 fastv COVID-19
updated 15 days ago by 38k • written 3.0 years ago by ★ 2.4k
60
votes
52
replies
39k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 15 days ago by 38k • written 6.5 years ago by ★ 3.3k
11
votes
7
replies
4.5k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 15 days ago by 38k • written 2.5 years ago by 84k
18
votes
22
replies
7.1k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 15 days ago by 38k • written 3.3 years ago by 7.8k
113 results • Page 1 of 3
Recent Votes
STARsolo config for 10x Chromium v1, v2, v3
Answer: How to remove unknown batch-batch effects from GEO datasets
Any tips in landing a bioinformatic job?
A: correlation between SCRNA-Seq and bulk RNAseq
correlation between SCRNA-Seq and bulk RNAseq
Comment: How to remove unknown batch-batch effects from GEO datasets
Comment: Aberrant splicing in bulk RNAseq
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Answer: extract gene coordinates and TSS from gene list by Carlo Yague 8.3k
I'm not going to give you a complete answer, but you can start looking at this posts: https://www.biostars.org/p/147351/ And use the [R …
Comment: How to make "Custom annotation File" for GO analysis using TOPgo by Shred ★ 1.1k
Do not post screenshots: instead use some lines of input and the desired output.
Comment: Snakemake doesn't recognize output files even though they are created by Shred ★ 1.1k
Sorry but I'm not able to properly understand your scenario. Did your pipeline complete the dry run?
Comment: How to remove unknown batch-batch effects from GEO datasets by 2317711200 • 0
Thank you very much for your response.
Answer: How to remove unknown batch-batch effects from GEO datasets by Gordon Smyth ★ 5.6k
removeBatchEffect() wouldn't produce the outlier effect that you show on the right unless there was something seriously wrong with the batc…
Answer: How to get subset of a Seurat object based on metadata? by fracarb8 ▴ 940
To keep the subset call as clean as possible, you can: Idents(skin) <- "predicted_cell_type" cell_values <- c("0:CD8 T cell") …
Answer: How to remove unknown batch-batch effects from GEO datasets by 2317711200 • 0
R codes： library(tidyverse) ####数据获取#### #引文 #citation(package = "GEOquery") #数据提取 GSE53625_matrix<-GEOquery::getGEO(GEO = "GSE5362…
Answer: Any tips in landing a bioinformatic job? by iraun 5.9k
Hi Jorge! In addition to what has already been said, I found my first bioinformatics job in Spain (Barcelona), using this webpage: [http…
Comment: How to remove unknown batch-batch effects from GEO datasets by 2317711200 • 0
It is a great honor to receive your response. The data in question is sourced from GSE53625. While using arrayQualityMetrics to assess the…
Answer: Extract data from Signac RegionMatrix? by Chironex ▴ 40
object@assays$ATAC@positionEnrichment$my_region_matrix and also object@assays$ATAC@positionEnrichment$my_region_matrix$condit…
Comment: Any tips in landing a bioinformatic job? by ATpoint 70k
Great answer, narrowing it down the the key points!
Comment: How to remove unknown batch-batch effects from GEO datasets by ATpoint 70k
The righthand plot might be totally fine once you remove that one outlier on the left, try that first. The batch effect manifesting along P…
Comment: using CITE-seq data to cluster single cells by ATpoint 70k
If it is really just two genes then why not just plotting logcounts of gene1 vs logcounts of gene2 as in a FACS scatter plot and see whethe…
Comment: How to remove unknown batch-batch effects from GEO datasets by 2317711200 • 0
As a beginner, I hope to receive professional answers. If necessary, I can provide rewards and R code.
Answer: Align miRNA library (small RNA-seq) without trimming by ATpoint 70k
For miRNA you should trim the data to the actual expected miRNA length (20-something bp, I would need to look up the exact value). Reason i…
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