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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
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
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
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
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
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
74
votes
13
replies
65k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r cancer classification
updated 4 months ago by 38k • written 9.4 years ago by ★ 1.2k
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
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
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
80
votes
2
replies
53k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 4 weeks ago by 38k • written 9.8 years ago by 11k
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
0
votes
3
replies
47k
views
Tutorial: Installation VMD on LINUX_64
VMD VMD installation gromacs Tutorial
updated 6.8 years ago by 52k • written 6.8 years ago by ▴ 10
65
votes
9
replies
47k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 7 weeks ago by 38k • written 9.8 years ago by ★ 3.0k
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
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
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
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
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
45
votes
2
replies
35k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 5 weeks ago by 38k • written 11.0 years ago by ▴ 540
70
votes
3
replies
34k
views
Tutorial: Revisiting the FastQC read duplication report
fastqc
updated 16 months ago by 38k • written 8.7 years ago by 97k
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
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
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
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
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
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
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 9.5 years ago by ★ 7.7k
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
99
votes
8
replies
27k
views
8 follow
Tutorial: Guide to TCGA data
TCGA cancer tools RNA-Seq clinical Tutorial
updated 6.3 years ago by ▴ 250 • written 7.1 years ago by ★ 1.1k
31
votes
12
replies
26k
views
7 follow
Tutorial: So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control fastqc
updated 29 days ago by 38k • written 9.5 years ago by 97k
67
votes
6
replies
24k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 5 weeks ago by 38k • written 10.6 years ago by 97k
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
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
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
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
51
votes
3
replies
22k
views
Tutorial: Sam File Format - Lesser Known Tips And Tricks
sam
updated 4 weeks ago by 38k • written 10.2 years ago by ▴ 300
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
30
votes
6
replies
21k
views
Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 6 months ago by 38k • written 10.9 years ago by 97k
1
vote
1
reply
19k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 8 months ago by ★ 2.6k • written 8 months ago by ▴ 10
10
votes
5
replies
18k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 15 days ago by 38k • written 4.7 years ago by ★ 9.3k
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
41
votes
6
replies
18k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 14 months ago by ▴ 40 • written 2.0 years ago by 11k
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
42
votes
2
replies
17k
views
Tutorial: Sequencing Technology Review Papers
sequencing papers
updated 5 weeks ago by 38k • written 10.6 years ago by 97k
39
votes
6
replies
17k
views
Tutorial: Creating chromosome karyotype plot with R and ggplot2
chromosome karyotype R ggplot2 Tutorial
updated 5.4 years ago by ★ 3.4k • written 5.6 years ago by ★ 3.3k
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
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
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
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
353 results • Page 1 of 8
Recent Votes
A: pulling snps from vcf file using ids
pulling snps from vcf file using ids
how to retrieve mouse (mm10) gene information from Ensemble using Biomart inR
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
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Recent Replies
Answer: ChIPseeker Warning Message by ATpoint 70k
That happens when you merge or compare GRanges objects that have different chromosomes in it. Either your input or the content from org.Mm.…
Comment: extract gene coordinates and TSS from gene list by Chironex ▴ 40
thank you, I was able to get the coordinates of the gene, but I need to extract the TSS and extend it to 1000 bp.
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…
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