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327 results • Page 1 of 7
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282
votes
39
replies
173k
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 3 months ago by 40k • written 8.1 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 10 weeks ago by • 0 • written 5.2 years ago by ▴ 580
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
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
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
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 9.8 years ago by ★ 1.2k
149
votes
35
replies
60k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 6 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 6 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 6 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 23 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
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
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
32k
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 12 weeks 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 8 weeks ago by • 0 • written 7.5 years ago by 20k
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 5.0 years ago by 16k
51
votes
3
replies
22k
views
Tutorial: Sam File Format - Lesser Known Tips And Tricks
sam
updated 6 months ago by 40k • written 10.7 years ago by ▴ 300
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 3 months ago by • 0 • written 5.2 years ago by ★ 1.3k
72
votes
48
replies
16k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs alignment bwa
updated 6 months ago by 40k • written 10.6 years ago by 33k
35
votes
17
replies
16k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning classification
updated 4 months ago by 134k • written 9.8 years ago by 20k
30
votes
14
replies
16k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
genome-music linux smg
updated 6 months ago by 40k • written 10.6 years ago by 6.0k
75
votes
14
replies
15k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 7 months ago by 40k • written 10.3 years ago by 9.7k
15
votes
5
replies
15k
views
Tutorial: How to create a mutation lolliplot with GenVisR
bioconductor graphics R genvisr
updated 5 months ago by 40k • written 7.3 years ago by 20k
54
votes
5
replies
14k
views
6 follow
Tutorial: Machine Learning For Cancer Classification - Part 4 - Plotting A Kaplan-Meier Curve For Survival Analysis
r
updated 11 months ago by 40k • written 9.8 years ago by ★ 1.2k
327 results • Page 1 of 7
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A: How To Extract A Sequence From A Big (6Gb) Multifasta File ?
A: How to extract a sequence below a fasta header (">") from a fasta file ?
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Answer: How to find positions with higher depth relative to their surroundings by xiaoguang ▴ 120
I saw you want to get regions that have significantly higher depth than their surroundings; you must get a p-value to show significant as w…
Comment: how to calculate BAF and LRR from VCF or BCF files? by xiaoguang ▴ 120
Hi, The ASCAT new version has introduced a new function called `ascat.prepareHTS`, which can be used to prepare all files that are required…
Comment: GERP++ (gerpcol) error on a test data by Diana • 0
I solved the problem in the end. I was under the impression that the reference sequence had to be provided in a separate fasta file: c…
Answer: How to find positions with higher depth relative to their surroundings by d-cameron ★ 2.9k
The usual way of doing this is to use one of the many existing copy number variant caller. Doing this yourself is both a) complicated to do…
Answer: How to retrieve LoF and missense variants in WES data? by luffy ▴ 30
@ _quantum_girl_, as Pierre mentioned, you can annotate your VCF with [snpEff][1] or [ensembl vep][2] once you annotated you could filter n…
Comment: Adding a control sample to bulk RNA-seq by Chris ▴ 180
Thank you so much! It is from the same lab but from another project. Would you please explain about combining the counts together a little …
Answer: Importance of Data Structures for Bioinformatics? by d-cameron ★ 2.9k
> how important are Data Structures to multi-omic / bioinformatic analysis Generally speaking, they're not critical if you are using an …
Answer: Recommended order of operations for identifying the genomic location and copy-nu by dk0319 ▴ 70
Update: The above workflow was successful, in that contig_1719 does contain approximately 4 copies of my insert based on searching pieces o…
Comment: manhattan plot with vcf information by sooni ▴ 10
I want to find out specific genes using the manhattan plot. I divide the patients into two groups, controls and patients, and try to identi…
Comment: Importance of Data Structures for Bioinformatics? by dsull ★ 4.6k
If you don't want to hurt your GPA, why not just take the course pass/fail or, if that's not an option, simply audit it? I doubt anyone wi…
Comment: How to DESeq2 using miRNA data obtained using TCGAbiolinks by swbarnes2 13k
miRNAs are rather small, and your typical RNASeq library prep will remove small sequences. Are you sure that the data you are trying to ge…
Comment: Inflated GWAS test statistic after merging multiple batches of genotype dataset by LauferVA 3.7k
even these measures will very often not fix the problem in the context of a problem of a problem of perfect separation such as OP describes.
Comment: Inflated GWAS test statistic after merging multiple batches of genotype dataset by LauferVA 3.7k
Hi Amy, I understand, this is why I said, > "The degree to which this is possible depends on the relative content > of each study - e.g. …
Answer: What is the difference between norm --multiallelics -any versus --atomize? by Ram 40k
I don't think atomization compares to norm with respect to multiallelic sites. You can see an example of atomatization on a multi-allelic s…
Comment: How to display all top markers in the heatmap by DoHeatmap (Seurat) when there a by alwayshope ▴ 30
Great guidance! Thank you very much!
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