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323 results • Page 2 of 7
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45
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14
replies
65k
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10 follow
Tutorial: Using R in Conda
R
updated 11 weeks ago by 39k • written 2.9 years ago by ▴ 690
7
votes
14
replies
2.4k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 7 months ago by • 0 • written 15 months ago by ▴ 30
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 7 months ago by 39k • written 9.5 years ago by ★ 1.2k
3
votes
13
replies
10k
views
Tutorial: Merging multiple vcf files into Single vcf file
merge vcf bcftools
updated 11 weeks ago by 39k • written 4.3 years ago by ▴ 140
17
votes
13
replies
1.7k
views
Tutorial: Screen shots of text (please don't)!
meta
updated 19 days ago by 39k • written 6.2 years ago by 52k
31
votes
12
replies
27k
views
7 follow
Tutorial: So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control fastqc
updated 3 months ago by 39k • written 9.6 years ago by 98k
8
votes
12
replies
6.2k
views
Tutorial: Create your own VPN to access work resources from home
tinyproxy OpenVPN VPN
updated 7 weeks ago by 39k • written 7.0 years ago by 13k
16
votes
11
replies
13k
views
7 follow
Tutorial: retrieve full TCGA datasets from cBioportal with R
TCGA RNA-seq data-retrieval cBioportal R
updated 11 weeks ago by 39k • written 6.6 years ago by ★ 4.6k
16
votes
11
replies
7.4k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
11 weeks ago by Ram 39k
6
votes
11
replies
4.7k
views
6 follow
Tutorial: Add count numbers to headers in a fasta file
genome
updated 3 months ago by 39k • written 6.5 years ago by ▴ 50
12
votes
11
replies
6.7k
views
Tutorial: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI Bioproject SRA BioSample
updated 20 days ago by 39k • written 6.2 years ago by ★ 2.4k
6
votes
10
replies
4.4k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 11 weeks ago by 39k • written 5.3 years ago by ▴ 360
21
votes
10
replies
5.2k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 11 weeks ago by 39k • written 2.7 years ago by 12k
26
votes
10
replies
63k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 11 weeks ago by 39k • written 2.2 years ago by ★ 1.3k
9
votes
9
replies
3.7k
views
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
reference-coverage ngs
updated 14 days ago by 39k • written 5.7 years ago by 85k
65
votes
9
replies
47k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 3 months ago by 39k • written 9.9 years ago by ★ 3.0k
16
votes
9
replies
4.6k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 11 months ago by ▴ 70 • written 18 months ago by ★ 1.1k
8
votes
9
replies
10k
views
Tutorial: Extracting subset of records from FASTA/FASTQ files based on exact/pattern matches of IDs (ONE-LINERS)
fastq fasta
updated 12 weeks ago by 39k • written 9.1 years ago by ★ 1.8k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 12 weeks ago by 39k • written 9.1 years ago by ★ 1.9k
14
votes
9
replies
4.2k
views
6 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
aspera ascp
updated 25 days ago by • 0 • written 11 months ago by 72k
19
votes
9
replies
6.1k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 3 months ago by 39k • written 10.0 years ago by 9.6k
31
votes
9
replies
26k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 11 weeks ago by 39k • written 2.8 years ago by ▴ 140
81
votes
8
replies
8.0k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop lectures genomics training
updated 12 weeks ago by 39k • written 9.0 years ago by 19k
30
votes
8
replies
10k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
python pipeline
updated 12 weeks ago by 39k • written 9.1 years ago by ▴ 800
7
votes
8
replies
3.0k
views
Tutorial: Determine if a transcription factor is bound with CENTIPEDE
ChIP-Seq transcription-factor DNase-Seq CENTIPEDE
updated 5 months ago by 39k • written 7.9 years ago by ★ 2.2k
99
votes
8
replies
27k
views
8 follow
Tutorial: Guide to TCGA data
cancer RNA-Seq clinical TCGA
updated 8 weeks ago by 39k • written 7.3 years ago by ★ 1.1k
38
votes
8
replies
10k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 11 weeks ago by 39k • written 2.7 years ago by 2.9k
16
votes
7
replies
13k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 11 weeks ago by 39k • written 4.0 years ago by ▴ 310
11
votes
7
replies
13k
views
Tutorial: Removing rows with duplicate values based on 1 or more key values - linux awk
awk linux bash
updated 14 days ago by 39k • written 5.7 years ago by 85k
14
votes
7
replies
5.6k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq peaks R HOMER
updated 11 weeks ago by 39k • written 7.0 years ago by ★ 3.3k
48
votes
7
replies
11k
views
7 follow
Tutorial: Genome Assembly Review Papers
assembly papers
updated 3 months ago by 39k • written 10.8 years ago by 98k
12
votes
7
replies
4.8k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 11 weeks ago by 39k • written 2.7 years ago by 85k
10
votes
7
replies
1.3k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
8 weeks ago by barslmn ★ 1.5k
11
votes
7
replies
7.2k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 11 days ago by 39k • written 2.2 years ago by ▴ 300
20
votes
7
replies
5.7k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2 RNA-Seq R
updated 11 weeks ago by 39k • written 4.6 years ago by ▴ 750
31
votes
6
replies
9.4k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 11 weeks ago by 39k • written 3.0 years ago by 85k
67
votes
6
replies
25k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 3 months ago by 39k • written 10.8 years ago by 98k
39
votes
6
replies
17k
views
Tutorial: Creating chromosome karyotype plot with R and ggplot2
ggplot2 R chromosome karyotype
updated 14 days ago by 39k • written 5.8 years ago by ★ 3.3k
16
votes
6
replies
5.8k
views
Tutorial: How to make your snakefiles self-documenting
snakemake
updated 7 weeks ago by 39k • written 6.6 years ago by ★ 1.7k
60
votes
6
replies
9.0k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 3 months ago by 39k • written 9.8 years ago by 9.6k
43
votes
6
replies
11k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 12 weeks ago by 39k • written 9.3 years ago by 5.9k
13
votes
6
replies
5.3k
views
Tutorial: Trim & align paired-end reads in a single pass
align trim fastq pipe paired-end
updated 7 weeks ago by 39k • written 6.9 years ago by 14k
2
votes
6
replies
2.8k
views
Tutorial: Rembrandt Glioma Data Analysis (PART I) - Are Gender specific genes related to cancer ?
gene R Rembrandt
updated 7 weeks ago by 39k • written 6.9 years ago by ▴ 140
30
votes
6
replies
21k
views
Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 8 months ago by 39k • written 11.1 years ago by 98k
101
votes
6
replies
23k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 11 weeks ago by 39k • written 4.7 years ago by 16k
11
votes
6
replies
4.6k
views
Tutorial: sharing some naive codes for microarray normalization in R with whom are too new in R alike me
R
updated 10 months ago by 39k • written 7.3 years ago by ★ 4.2k
20
votes
6
replies
5.0k
views
Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 11 weeks ago by 39k • written 6.7 years ago by ★ 5.2k
5
votes
5
replies
6.1k
views
Tutorial: use firehose_get to download TCGA data
tcga RNA-Seq
updated 13 days ago by 39k • written 5.6 years ago by ▴ 130
12
votes
5
replies
1.9k
views
Tutorial: FASTA file split
fasta
updated 11 weeks ago by 39k • written 3.0 years ago by 7.9k
2
votes
5
replies
2.0k
views
Tutorial: Building OMA database on SGE
oma
updated 7 weeks ago by 39k • written 6.9 years ago by ▴ 10
323 results • Page 2 of 7
Recent Votes
Answer: NCBI refseq ids to uniprot ids
Answer: NCBI refseq ids to uniprot ids
Comment: Unusual FASTQ file
Answer: Graphing Average Expression of Group of Genes
Comment: Graphing Average Expression of Group of Genes
How to create specific .bed files for a panel of genes
Answer: How do you add an ORF that overlaps the two regions where a circular genome is c
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Recent Replies
Answer: I don't want to believe the Interproscan DB estimated download time. by Mensur Dlakic ★ 23k
With [**aria2**][1] and multiple connections, I download at ~2.2MiB. The estimate is still ~190 hours. aria2c --continue=true --max-…
Comment: Seurat: How to get all genes name of a cell ? by jv ★ 1.2k
if you want the genes in your count matrix use `rownames(obj)`. Or are you looking to get all genes with count > 0 for a particular cell? P…
Comment: Unusual FASTQ file by Ram 39k
People from the middle east/indian subcontinent often associate the term "post title" with their job title, because a) post translates more…
Comment: How to make a dotplot for bulk RNA average expression ? by bhumm ▴ 40
I am not entirely clear on what you are trying to accomplish, but based on @Trivas answer, I would first transform the data relative to ave…
Answer: What is the best way to clean bulk RNA-seq data? by swbarnes2 13k
There really is no "best". Just find something reasonable, and document what you chose.
Comment: How to deal with duplicated gene IDs in TCGA RNA expression data? by Vincent Laufer ★ 2.8k
ok interesting. Do all, most, some, or a few of the genes have repeated lines. Is there a handy link to the exact file you are looking at?
Answer: Make a BedGraph file by bhumm ▴ 40
Bedtools window piped into genomecov? https://bedtools.readthedocs.io/en/latest/content/tools/window.html https://bedtools.readthedocs.io…
Answer: RNAseq Data and Pipeline by ATpoint 72k
STAR counts are the raw counts, that is appropriate for DESeq2.
Comment: RNAseq Data and Pipeline by swbarnes2 13k
STAR has a GeneCounts output that looks as you describe; three columns, depending on whether one thinks the prep is unstranded, or stranded…
Comment: RNAseq Data and Pipeline by Ram 39k
There is at least one more step that you haven't shared, isn't there? This line alone does not get you the data. You don't need to give us …
Comment: RNAseq Data and Pipeline by turcoa1 • 0
my entire code is not done. All I am trying to understand is if the STAR - counts downloaded from this query have raw reads. There are head…
Comment: RNAseq Data and Pipeline by Ram 39k
Please provide your entire code so those of us wishing to do a quick test can download and check for ourselves. Also, please use the format…
Comment: RNAseq Data and Pipeline by turcoa1 • 0
```r query <- GDCquery( project = "TCGA-THCA", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantificatio…
Comment: NCBI Common Taxonomy Tree by GenoMax 129k
It may be best to email NCBI help desk with these questions. Post their response here once you hear back from them.
Comment: RNAseq Data and Pipeline by Ram 39k
What data are you downloading? Can you show us your GDCquery commands please?
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