Limit : all time
all time today this week this month this year
353 results • Page 1 of 8
Sort: replies
Rank Views Votes Replies
238
votes
176
replies
84k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 5 months ago by 38k • written 7.7 years ago by ★ 4.6k
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
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
75
votes
70
replies
16k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 15 days ago by 38k • written 5.1 years ago by 84k
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
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
72
votes
60
replies
23k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 6 weeks ago by 38k • written 5.6 years ago by 84k
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
72
votes
48
replies
15k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs alignment bwa
updated 4 weeks ago by 38k • written 10.1 years ago by 33k
194
votes
44
replies
68k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 11 weeks ago by 38k • written 10.5 years ago by 20k
59
votes
43
replies
18k
views
18 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign pacbio arrow smrt-limk
updated 15 days ago by 38k • written 5.5 years ago by ★ 1.4k
78
votes
41
replies
28k
views
24 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 4 months ago by • 0 • written 9.4 years ago by ★ 7.7k
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
276
votes
39
replies
164k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 5 days ago by 38k • written 8.6 years ago by 20k
146
votes
35
replies
58k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 4 weeks ago by 38k • written 10.3 years ago by ★ 1.6k
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
145
votes
34
replies
51k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 4 weeks ago by 38k • written 10.0 years ago by 5.9k
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
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
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
82
votes
28
replies
28k
views
19 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 6 weeks ago by 38k • written 7.1 years ago by 20k
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
68
votes
26
replies
24k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 27 days ago by 38k • written 9.1 years ago by 97k
64
votes
26
replies
11k
views
7 follow
Tutorial: Parallel processing in R
biocparallel mclapply foreach R
updated 15 days ago by 38k • written 5.5 years ago by 84k
94
votes
25
replies
31k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 5 weeks ago by 38k • written 10.5 years ago by 97k
136
votes
25
replies
75k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 11 months ago by 38k • written 10.9 years ago by ★ 4.2k
58
votes
25
replies
36k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 12 days ago by 38k • written 6.7 years ago by ★ 9.3k
9
votes
23
replies
8.3k
views
7 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
orthomcl ubuntu linux mysql Tutorial
4.8 years ago by vimalkvn ▴ 310
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
142
votes
21
replies
29k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 10 months ago by 38k • written 8.3 years ago by ★ 1.6k
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
82
votes
21
replies
71k
views
13 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 5 weeks ago by ★ 2.9k • written 4.7 years ago by ▴ 540
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
47
votes
19
replies
12k
views
8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control fastqc
updated 11 weeks ago by 38k • written 10.1 years ago by 97k
23
votes
19
replies
5.7k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
mutation fastq cancer target Tutorial
updated 5.2 years ago by • 0 • written 6.5 years ago by ★ 2.4k
51
votes
19
replies
41k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization bigwig chip-seq rna-seq
updated 5 weeks ago by 38k • written 11.0 years ago by 11k
8
votes
19
replies
12k
views
9 follow
Tutorial: A:orthomcl with local mysql server on linux server, complete install
mysql orthomcl
updated 20 days ago by 38k • written 8.4 years ago by ▴ 580
42
votes
19
replies
7.1k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 4 weeks ago by 38k • written 10.1 years ago by 4.1k
89
votes
19
replies
30k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray bioconductor expression classification
updated 28 days ago by 38k • written 9.4 years ago by 20k
8
votes
17
replies
2.3k
views
Tutorial: Simple approach to RNA-seq (T-Bioinfo platform)
alignment next-gen-sequencing RNA-seq
updated 7 months ago by 38k • written 7.5 years ago by ▴ 340
12
votes
17
replies
2.2k
views
Tutorial: How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola bwa
updated 3 months ago by 38k • written 7.8 years ago by 97k
26
votes
17
replies
6.7k
views
8 follow
Tutorial: virtualenv - running Python based software in isolation
python virtualenv
updated 6 months ago by 38k • written 8.6 years ago by 5.9k
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
33
votes
16
replies
15k
views
10 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning classification
updated 28 days ago by 38k • written 9.4 years ago by 20k
42
votes
16
replies
21k
views
15 follow
Tutorial: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC varscan2 CNV copy-number
updated 7 months ago by 38k • written 7.5 years ago by ★ 2.3k
34
votes
15
replies
18k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 14 days ago by 38k • written 6.5 years ago by ▴ 310
34
votes
15
replies
5.1k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 15 days ago by 38k • written 3.8 years ago by ★ 9.3k
24
votes
15
replies
7.9k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
course training mooc
updated 4 weeks ago by 38k • written 10.2 years ago by 9.5k
59
votes
15
replies
11k
views
Tutorial: Which human reference genome should I use?
genome alignment assembly Tutorial
4.4 years ago by finswimmer 16k
7
votes
14
replies
2.1k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 5 months ago by • 0 • written 13 months ago by ▴ 30
353 results • Page 1 of 8
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
Recent Locations • All
rome, 2 minutes ago
United Kingdom, 3 minutes ago
Germany, 6 minutes ago
India, 7 minutes ago
EMBL-EBI, 9 minutes ago
Republic of Ireland, 9 minutes ago
Dartmouth College, 10 minutes ago
Recent Awards • All
Popular Question to Bogdan ★ 1.3k
Popular Question to pavelasquezv ▴ 50
Popular Question to Anand Rao ▴ 550
Scholar to andres.firrincieli 3.2k
Scholar to Jesse • 0
Popular Question to chaco001 ▴ 10
Scholar to Jaykumar ▴ 50
Recent Replies
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…
Comment: boxplot issue by ATpoint 70k
Please get used to make your question reproducible and precise, meaning provide example data and reduce code to a minimum.
Traffic: 2308 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6