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Tutorial: Using the MinION MinKNOW software on Ubuntu 1604
long-reads oxford-nanopore minion
updated 8 months ago by 41k • written 4.4 years ago by 5.8k
0
votes
0
replies
1.2k
views
Tutorial: Training GeneMark-EP+ ab-initio tool
abinitio training genemark annotation
updated 8 months ago by 41k • written 3.8 years ago by 8.4k
2
votes
1
reply
3.0k
views
Tutorial: How to extract and filter SNP data from the genotyping-by-sequencing (GBS) data in vcf format using bcftools
bcftools SNP-Filtering VCF
updated 8 months ago by 41k • written 3.8 years ago by ▴ 10
5
votes
0
replies
3.1k
views
Tutorial: How to run CWL with Nextflow
cwl nextflow
updated 8 months ago by 41k • written 3.8 years ago by ★ 3.4k
5
votes
2
replies
2.2k
views
Tutorial: Using Bedtools Closest (closestBed) to make distance histograms of protein binding frequency near all types of pre-RNA junctions (e.g. exon-intron an…
preRNA closestBed bedtools-closest bedtools
updated 8 months ago by 41k • written 4.9 years ago by ▴ 10
50
votes
3
replies
4.5k
views
Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 8 months ago by 41k • written 4.9 years ago by 78k
21
votes
9
replies
6.4k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 9 months ago by 41k • written 10.5 years ago by 9.7k
282
votes
39
replies
177k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 8 months ago by 41k • written 9.3 years ago by 20k
64
votes
26
replies
13k
views
7 follow
Tutorial: Parallel processing in R
biocparallel mclapply foreach R
updated 8 months ago by 41k • written 6.2 years ago by 86k
34
votes
15
replies
6.0k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 8 months ago by 41k • written 4.5 years ago by ★ 9.3k
20
votes
4
replies
2.5k
views
Tutorial: Bash One-liners collection on Github
bash linux shell
updated 8 months ago by 41k • written 4.6 years ago by ▴ 180
14
votes
7
replies
6.1k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq peaks R HOMER
updated 8 months ago by 41k • written 7.6 years ago by ★ 3.4k
2
votes
0
replies
4.5k
views
Tutorial: Calculation of TSS Scores for ATAC-seq Data
next-gen-sequencing
updated 8 months ago by 41k • written 4.4 years ago by ▴ 20
0
votes
0
replies
1.0k
views
Tutorial: Apply ALoFT to identify loss-of-function somatic or germline variants
ALoFT
updated 8 months ago by 41k • written 4.5 years ago by ★ 9.3k
16
votes
11
replies
14k
views
7 follow
Tutorial: retrieve full TCGA datasets from cBioportal with R
TCGA RNA-seq data-retrieval cBioportal R
updated 8 months ago by 41k • written 7.1 years ago by ★ 4.7k
10
votes
5
replies
21k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 8 months ago by 41k • written 5.4 years ago by ★ 9.3k
34
votes
15
replies
19k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 8 months ago by 41k • written 7.2 years ago by ▴ 310
6
votes
3
replies
4.4k
views
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment sequencing RNA-seq gene
updated 8 months ago by 41k • written 5.1 years ago by ▴ 40
0
votes
0
replies
1.0k
views
Tutorial: Introduction to Gen3 Webinar
gen3 open-source data-commons big-data
updated 8 months ago by 41k • written 4.8 years ago by ▴ 310
0
votes
1
reply
1.3k
views
Tutorial: SFA (Stochastic Frontier Analysis) Frontier 4.1
r spss
updated 8 months ago by 41k • written 5.8 years ago by ▴ 10
4
votes
2
replies
3.5k
views
Tutorial: Introduce OpenGene: an open source library for processing NGS data
NGS sequencing Julia OpenGene
updated 8 months ago by 41k • written 7.8 years ago by ★ 2.5k
28
votes
4
replies
4.2k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 8 months ago by 41k • written 4.9 years ago by 26k
61
votes
6
replies
9.3k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 9 months ago by 41k • written 10.3 years ago by 9.7k
4
votes
0
replies
949
views
Tutorial: Finding individual motif occurrences with FIMO from the MEME suite
motif meme jaspar fimo
updated 8 months ago by 41k • written 5.0 years ago by 78k
5
votes
2
replies
2.2k
views
Tutorial: NCBI submissions: SRA and TSA
NCBI TSA SRA RNA-Seq
updated 8 months ago by 41k • written 5.0 years ago by ▴ 50
6
votes
0
replies
1.5k
views
Tutorial: NCBI dbVar releases updated human reference structural variation (SV) data files and tutorials
dbvar structural-variation
updated 8 months ago by 41k • written 5.1 years ago by ▴ 70
32
votes
4
replies
7.3k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 8 months ago by 41k • written 5.1 years ago by ★ 1.6k
58
votes
25
replies
39k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 8 months ago by 41k • written 7.4 years ago by ★ 9.3k
63
votes
15
replies
13k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 6 months ago by 41k • written 5.2 years ago by 16k
3
votes
4
replies
3.5k
views
Tutorial: Gene Set Enrichment Analysis on T-BioInfo
gene RNA-Seq
updated 6 months ago by 41k • written 5.1 years ago by ▴ 340
22
votes
2
replies
5.8k
views
Tutorial: Use a workflow management tool to manage your computational pipelines
workflow-management snakemake pipeline
updated 8 months ago by 41k • written 7.1 years ago by ★ 2.1k
1
vote
2
replies
3.2k
views
Tutorial: Standalone BLAST error: UnexpectedTagClassByte
software-error blast
updated 13 months ago by 41k • written 8.4 years ago by ▴ 10
10
votes
4
replies
3.4k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 6 months ago by 41k • written 5.8 years ago by 86k
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 13 months ago by 41k • written 10.1 years ago by ★ 1.2k
20
votes
4
replies
14k
views
Tutorial: How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor affymetrix
updated 9 months ago by 41k • written 10.7 years ago by 20k
0
votes
0
replies
1.2k
views
Tutorial: In the cloud - Guide to running VerifyBamID to estimate DNA sample contamination
sequence cloud dna sequencing
updated 6 months ago by 41k • written 5.4 years ago by • 0
20
votes
2
replies
7.8k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 6 months ago by 41k • written 6.0 years ago by ★ 3.4k
2
votes
0
replies
1.3k
views
Tutorial: Principal Component Analysis (PCA ON T-BIOINFO)
RNA-Seq next-gen
updated 6 months ago by 41k • written 5.5 years ago by ▴ 340
1
vote
4
replies
3.2k
views
Tutorial: Applying machine learning to NGS transcriptomic data
next-gen RNA-Seq
updated 6 months ago by 41k • written 5.6 years ago by ▴ 340
3
votes
4
replies
4.3k
views
Tutorial: gencore: a tool to reduce sequencing noises by generating consensus reads
consensus OpenGene sequencing-noise
updated 6 months ago by 41k • written 5.6 years ago by ★ 2.5k
18
votes
2
replies
5.8k
views
Tutorial: Update kraken databases
database kraken k-mer python
updated 6 months ago by 41k • written 6.6 years ago by 5.3k
2
votes
0
replies
1.5k
views
Tutorial: Webinar: Extracting research evidence from publications
text-mining ontology pubmed
updated 6 months ago by 41k • written 5.8 years ago by ▴ 60
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 9 months ago by 41k • written 10.6 years ago by 6.0k
1
vote
0
replies
2.3k
views
Tutorial: Tutorial DEAP 2.1 In DOS
deap2.1 R
updated 8 months ago by 41k • written 5.8 years ago by ▴ 10
0
votes
0
replies
3.5k
views
Tutorial: SFA (Stochastic Frontier Analysis) STATA 14
R
updated 6 months ago by 41k • written 5.8 years ago by ▴ 10
0
votes
0
replies
1.5k
views
Tutorial: PLS SEM (Partial Least Square Sructural Equation Modeling) Analysis WarpPLS 6
R
updated 6 months ago by 41k • written 5.8 years ago by ▴ 10
3
votes
0
replies
2.2k
views
Tutorial: Deep Learning for Cancer Immunotherapy
keras tensorflow
updated 6 months ago by 41k • written 5.9 years ago by 22k
0
votes
0
replies
1.5k
views
Tutorial: MWD (Mackinnon, White And Davidson) In R
R
updated 6 months ago by 41k • written 5.9 years ago by ▴ 10
0
votes
0
replies
2.1k
views
Tutorial: Transforming (Transformation) Data LN, Log, SQRT In R Commander
R
updated 6 months ago by 41k • written 5.9 years ago by ▴ 10
14
votes
2
replies
2.3k
views
Tutorial: Exploring OpenSNP - an RMarkdown report on crowdsourced genotypes and phenotypes
SNP R
updated 8 months ago by 41k • written 7.7 years ago by 22k
384 results • Page 4 of 8
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A: How to do DMR analysis with BiSeq (for RRBS methylation data)?
A: How to do DMR analysis with BiSeq (for RRBS methylation data)?
Answer: 1000 genomes data?
Answer: General question about clustering in scRNAseq
Answer: General question about clustering in scRNAseq
A: Cluster sub-set analysis using Seurat
A: Cluster sub-set analysis using Seurat
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Recent Replies
Comment: How to avoid missannotated GO terms? by Dr.Animo ▴ 80
These kind of missannotations are assigned to multiple plant proteins except few like Arabidopsis thaliana and Zea maize. The problem is if…
Answer: SQL request from NCBI metadata and stat_analysis tables by zorbax ▴ 600
I think what you are looking for is the LEFT JOIN approach, where you can select a specific phylum. Have you tried this (next you should or…
Comment: Convert NCBI Downloaded files to ANNOVAR format by Ram 41k
You may also find tools such as vcfanno and bcftools easier to work with, if you don't want to spend too much time reformatting dictionary …
Comment: Convert NCBI Downloaded files to ANNOVAR format by robert • 0
Ok I guess I got confused because there is support for, for example gff3-solid, but not directly gff files. I will have a look at VEP, but …
Comment: How to perform quality control for sex when there are no variants after threshol by kl ▴ 10
I am trying with PLINK --check sex. Would an option be to merge my data with 1000 genomes European allele frequencies and redo the threshol…
Comment: Convert NCBI Downloaded files to ANNOVAR format by Ram 41k
The documentation is clear on this: `convert2annovar.pl` is used to convert input (genotype) files to ANNOVAR format. It is not used on dic…
Comment: How to perform quality control for sex when there are no variants after threshol by Ram 41k
The simple answer is you can't. Also, is there a reason why your title and your post body have the same content? Use a concise title and el…
Comment: Differential expression using Bowtie2 by ATpoint 78k
You cannot just randomly pull data from NCBI and then quantitatively compare them. RNA-seq is inherently a relative measure and quantitativ…
Comment: how to remove multiple columns from a file in R by Ram 41k
Accept their answer and then add your own and accept that as well.
Comment: how to remove multiple columns from a file in R by Ram 41k
Please stop asking basic R/programming questions and use Google to learn the underlying concepts. A simple search is the way to start: http…
Answer: get gene name from rsID by Ram 41k
Not all variants fall in coding regions. `rs2873296` for example is `NC_000001.10:g.21721038A>G`, which is in a non-coding region.
Comment: Differential expression using Bowtie2 by 8d8fc19e • 0
NCBI's Sequence Read Archive gives me the transcriptome of an organ (the RNA-seq data) which can be downloaded either as a .fasta or .fastq…
Comment: Differential expression using Bowtie2 by ATpoint 78k
Which will be obtained from NCBI...what does that mean, and which data do you have?
Comment: fgsea leading edge genes by ATpoint 78k
Just check the rank of these genes in the ranked data that were input to fgsea, then you know.
Answer: fgsea leading edge genes by Yuri ★ 1.6k
I asked the same question myself. I looked at the code of `calcGseaStat` function in `fgsea` package, and it appears that leading edge gene…
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