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282
votes
39
replies
174k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 6 months ago by 40k • written 9.1 years ago by 20k
288
votes
33
replies
99k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 6 months ago by 40k • written 9.9 years ago by 20k
238
votes
176
replies
88k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 4 months ago by 40k • written 8.2 years ago by ★ 4.7k
86
votes
22
replies
80k
views
14 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 11 weeks ago by • 0 • written 5.2 years ago by ▴ 580
137
votes
25
replies
79k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 17 months ago by 40k • written 11.4 years ago by ★ 4.2k
50
votes
14
replies
74k
views
10 follow
Tutorial: Using R in Conda
R
updated 6 months ago by 40k • written 3.2 years ago by ▴ 750
27
votes
10
replies
69k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 6 months ago by 40k • written 2.5 years ago by ★ 1.4k
196
votes
44
replies
69k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 8 months ago by 40k • written 11.0 years ago by 20k
75
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 10 months ago by 40k • written 9.9 years ago by ★ 1.2k
149
votes
35
replies
60k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 7 months ago by 40k • written 10.8 years ago by ★ 1.6k
85
votes
2
replies
56k
views
6 follow
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 7 months ago by 40k • written 10.2 years ago by 11k
146
votes
34
replies
53k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 7 months ago by 40k • written 10.4 years ago by 6.0k
0
votes
3
replies
50k
views
Tutorial: Installation VMD on LINUX_64
gromacs VMD
updated 5 months ago by 40k • written 7.3 years ago by ▴ 10
65
votes
9
replies
48k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 7 months ago by 40k • written 10.2 years ago by ★ 3.0k
146
votes
70
replies
46k
views
20 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 28 days ago by ▴ 260 • written 5.8 years ago by 86k
116
votes
66
replies
43k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 6 months ago by 40k • written 5.2 years ago by 76k
53
votes
19
replies
42k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization bigwig chip-seq rna-seq
updated 7 months ago by 40k • written 11.4 years ago by 11k
60
votes
52
replies
41k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 6 months ago by 40k • written 7.0 years ago by ★ 3.3k
2
votes
1
reply
40k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 14 months ago by 3.7k • written 14 months ago by ▴ 20
93
votes
105
replies
39k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 6 months ago by 40k • written 5.1 years ago by 86k
58
votes
25
replies
38k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 6 months ago by 40k • written 7.2 years ago by ★ 9.3k
72
votes
3
replies
36k
views
Tutorial: Revisiting the FastQC read duplication report
fastqc
updated 22 months ago by 40k • written 9.2 years ago by 98k
45
votes
2
replies
36k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 7 months ago by 40k • written 11.5 years ago by ▴ 540
132
votes
123
replies
33k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 6 months ago by ★ 1.1k • written 4.9 years ago by 86k
95
votes
25
replies
32k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 7 months ago by 40k • written 11.0 years ago by 98k
99
votes
16
replies
31k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 6 months ago by 40k • written 7.1 years ago by 26k
90
votes
19
replies
31k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray bioconductor expression classification
updated 6 months ago by 40k • written 9.9 years ago by 20k
82
votes
43
replies
30k
views
26 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 3 months ago by ▴ 40 • written 9.9 years ago by ★ 7.7k
33
votes
9
replies
30k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 6 months ago by 40k • written 3.1 years ago by ▴ 160
84
votes
29
replies
30k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 9 weeks ago by • 0 • written 7.5 years ago by 20k
142
votes
21
replies
29k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 16 months ago by 40k • written 8.8 years ago by ★ 1.6k
31
votes
12
replies
28k
views
7 follow
Tutorial: So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control fastqc
updated 6 months ago by 40k • written 9.9 years ago by 98k
99
votes
8
replies
28k
views
8 follow
Tutorial: Guide to TCGA data
cancer RNA-Seq clinical TCGA
updated 5 months ago by 40k • written 7.6 years ago by ★ 1.1k
71
votes
26
replies
26k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 6 months ago by 40k • written 9.6 years ago by 98k
67
votes
6
replies
25k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 7 months ago by 40k • written 11.1 years ago by 98k
73
votes
60
replies
25k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 7 months ago by 40k • written 6.0 years ago by 86k
104
votes
6
replies
24k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 6 months ago by 40k • written 5.1 years ago by 16k
42
votes
16
replies
22k
views
15 follow
Tutorial: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC varscan2 CNV copy-number
updated 13 months ago by 40k • written 8.0 years ago by ★ 2.4k
51
votes
3
replies
22k
views
Tutorial: Sam File Format - Lesser Known Tips And Tricks
sam
updated 7 months ago by 40k • written 10.7 years ago by ▴ 300
43
votes
6
replies
21k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 20 months ago by ▴ 40 • written 2.5 years ago by 12k
30
votes
6
replies
21k
views
Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 12 months ago by 40k • written 11.4 years ago by 98k
10
votes
5
replies
21k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 6 months ago by 40k • written 5.2 years ago by ★ 9.3k
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 6 months ago by 40k • written 6.0 years ago by ★ 1.4k
34
votes
15
replies
19k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 6 months ago by 40k • written 7.0 years ago by ▴ 310
84
votes
21
replies
18k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 6 months ago by 40k • written 2.9 years ago by 3.0k
39
votes
6
replies
18k
views
Tutorial: Creating chromosome karyotype plot with R and ggplot2
ggplot2 R chromosome karyotype
updated 4 months ago by 40k • written 6.1 years ago by ★ 3.3k
42
votes
2
replies
17k
views
Tutorial: Sequencing Technology Review Papers
sequencing papers
updated 7 months ago by 40k • written 11.1 years ago by 98k
76
votes
70
replies
17k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 6 months ago by 40k • written 5.6 years ago by 86k
18
votes
40
replies
17k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 6 months ago by 40k • written 7.2 years ago by ▴ 170
83
votes
34
replies
17k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 4 months ago by • 0 • written 5.3 years ago by ★ 1.3k
379 results • Page 1 of 8
Recent Votes
Comment: Quantification after transcriptome assembly with Trinity
Snakemake: output folder a as dependency to a different rule
A: Snakemake: output folder a as dependency to a different rule
A: In Seurat, How Do nCount_RNA Differ from nFeature_RNA?
How to identify 16s sequences from binning data(contigs)?
geom_signif() uses t-test to compare between more than 3 groups... Isn't this wrong?
Answer: Filter transcription factors
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Recent Replies
Answer: Gene enrichment analysis of prokaryotes gene by dthorbur ▴ 550
[Here](https://github.com/golden75/prokaryote_RNASeq) is a tutorial on how to use the R package DESeq2 for prokaryotic RNAseq analyses. …
Comment: Read block operation failed with BAM file by John Marshall 3.0k
Indeed, though it is a seek issue when accessing files over HTTP and other network protocols. So, unless there's something you didn't menti…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr by RM123 ▴ 10
Thank you for your help. I am comparing 4 groups, but as I have gene expression data I have a considerable number of boxplots to make. I fo…
Comment: gene correlations in between two groups by ATpoint 76k
And how should I know this? I cannot read minds, nor see your screen, data or anything. Please ask a good question with necessary details. …
Comment: gene correlations in between two groups by edus_bioinfo ▴ 40
Thanks. But they are already analyzed. Afaik it analyzes raw data. In my dataset for each gene there is score. I want to interpret the data…
Answer: GWAS phenotype by dthorbur ▴ 550
Hello again. Yes, you can conduct GWAS using binary trait data, but it comes with a whole suite of complications. See [this](https://ww…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr by RM123 ▴ 10
Hello Dariober, That seems like a good solution, however I'm pretty new to R. Could you tell me how I can do that?
Comment: how to create a loop in R by Nicolas Rosewick 10k
Not really a bioinformatics related question. Start by looking at R tutorial, there is plenty of them online e.g. : https://www.statmethods…
Comment: Violin plot (Monocle 3) - Troubleshooting by fracarb8 ★ 1.2k
You did not add the screenshot.
Answer: BED files by Alex Reynolds 35k
Generically via `bedmap`: ``` bedmap --echo --echo-map --count exome.bed annotations.bed > answer.bed ``` The `annotations.bed` fil…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr by dariober 14k
It seems to me that anova followed by HSD is a more sensible approach than applying independent t-tests. Granted this is the first time I s…
Comment: BED files by barslmn ★ 1.8k
I am guessing you want the annotation files. https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/
Comment: Filter human transcription factors by Alex Reynolds 35k
Curious how redundant these TFs are. Jeff Vierstra has done some analysis on this to simplify model sets: https://www.vierstra.org/resource…
Comment: Read block operation failed with BAM file by Alex Reynolds 35k
https://github.com/samtools/htslib/pull/1676 patches a seek issue in `htslib` (upon which `samtools` and `pysam` depend)
Comment: Merging the filename with tsv files for master file by barslmn ★ 1.8k
Could you add samples from your files and your expected output.
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