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238
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Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 13 days ago by 39k • written 7.8 years ago by ★ 4.6k
83
votes
34
replies
16k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 11 days ago by • 0 • written 5.0 years ago by ★ 1.3k
45
votes
28
replies
7.4k
views
9 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
20 days ago by Ram 39k
9
votes
23
replies
8.6k
views
7 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 19 days ago by 39k • written 5.4 years ago by ▴ 310
59
votes
15
replies
12k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 13 days ago by 39k • written 4.7 years ago by 16k
17
votes
13
replies
1.7k
views
Tutorial: Screen shots of text (please don't)!
meta
updated 27 days ago by 39k • written 6.2 years ago by 52k
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 28 days ago by 39k • written 6.2 years ago by ★ 2.4k
9
votes
9
replies
3.7k
views
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
reference-coverage ngs
updated 22 days ago by 39k • written 5.7 years ago by 85k
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 22 days ago by 39k • written 5.7 years ago by 85k
11
votes
7
replies
7.4k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 19 days ago by 39k • written 2.3 years ago by ▴ 300
39
votes
6
replies
17k
views
Tutorial: Creating chromosome karyotype plot with R and ggplot2
ggplot2 R chromosome karyotype
updated 22 days ago by 39k • written 5.8 years ago by ★ 3.3k
5
votes
5
replies
6.1k
views
Tutorial: use firehose_get to download TCGA data
tcga RNA-Seq
updated 21 days ago by 39k • written 5.6 years ago by ▴ 130
9
votes
5
replies
2.0k
views
Tutorial: What is new in samtools release 1.5 [Solstice Release] (21st June 2017)
samtools
updated 23 days ago by 39k • written 5.9 years ago by 98k
3
votes
4
replies
4.0k
views
Tutorial: gencore: a tool to reduce sequencing noises by generating consensus reads
consensus OpenGene sequencing-noise
updated 15 days ago by 39k • written 5.1 years ago by ★ 2.4k
3
votes
4
replies
3.4k
views
Tutorial: Gene Set Enrichment Analysis on T-BioInfo
gene RNA-Seq
updated 13 days ago by 39k • written 4.6 years ago by ▴ 340
10
votes
4
replies
2.9k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 19 days ago by 39k • written 5.3 years ago by 85k
1
vote
4
replies
3.0k
views
Tutorial: Applying machine learning to NGS transcriptomic data
next-gen RNA-Seq
updated 15 days ago by 39k • written 5.1 years ago by ▴ 340
3
votes
3
replies
8.0k
views
Tutorial: High Speed Downloading of SRA, SAM and Fastq Files
fastq sam Aspera-Connect sra
updated 20 days ago by 39k • written 5.5 years ago by ▴ 100
2
votes
3
replies
2.4k
views
Tutorial: It's about the journey, and not the destination
R network
updated 27 days ago by 39k • written 6.2 years ago by ★ 1.2k
5
votes
2
replies
2.8k
views
Tutorial: Get GC Content from UCSC with perl script (mysql)
myql ucsc gc-content perl
updated 27 days ago by 39k • written 6.2 years ago by ★ 9.3k
18
votes
2
replies
5.5k
views
Tutorial: Update kraken databases
database kraken k-mer python
updated 26 days ago by 39k • written 6.1 years ago by 5.2k
6
votes
2
replies
3.7k
views
Tutorial: GATK method for filtering vcf lines using GT values at all or multisample level.
genome vcf genotype variant-filtration
updated 26 days ago by 39k • written 6.0 years ago by ★ 1.5k
2
votes
2
replies
7.9k
views
Tutorial: Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ UMI fastp
updated 20 days ago by 39k • written 5.5 years ago by ★ 2.4k
20
votes
2
replies
7.2k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 20 days ago by 39k • written 5.5 years ago by ★ 3.4k
7
votes
2
replies
1.7k
views
Tutorial: Introduction to Human Genomics for Clinical Informaticists
genome
updated 22 days ago by 39k • written 5.8 years ago by ▴ 90
3
votes
2
replies
3.5k
views
Tutorial: Galaxy Tutorial on ChIP-seq
galaxy ChIP-Seq
updated 27 days ago by 39k • written 6.2 years ago by ▴ 30
11
votes
2
replies
7.4k
views
Tutorial: Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome plot coverage samtools
updated 27 days ago by 39k • written 6.2 years ago by ★ 1.5k
19
votes
2
replies
3.1k
views
Tutorial: Beginner's Handbook to Next Generation Sequencing
NGS
updated 27 days ago by 39k • written 6.2 years ago by ▴ 640
3
votes
2
replies
2.1k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences Workshops
updated 26 days ago by 39k • written 6.1 years ago by ▴ 100
10
votes
2
replies
3.4k
views
Tutorial: Graph visualization with igraph in R
Visualization igraph Graph R Network
updated 27 days ago by 39k • written 6.2 years ago by 26k
3
votes
1
reply
2.1k
views
Tutorial: Convert bam files to fastq in numbers as indicated in samtools flagstat stats.
samtools bam alignment fastq sequence
updated 26 days ago by 39k • written 6.0 years ago by ★ 1.5k
10
votes
1
reply
7.7k
views
Tutorial: How to select reads with specific flag using samtools
next-gen-sequencing
updated 22 days ago by 39k • written 5.8 years ago by ▴ 110
0
votes
1
reply
2.8k
views
Tutorial: Accessing sequences using batch entrez
genome
updated 21 days ago by 39k • written 5.6 years ago by • 0
7
votes
1
reply
2.0k
views
Tutorial: A gentle introduction to biogo
sequence golang biogo
updated 21 days ago by 39k • written 5.6 years ago by ★ 1.7k
0
votes
1
reply
1.7k
views
Tutorial: Nonparametric Regression STATA 15
STATA-15 Nonparametric-Regression STATA
updated 20 days ago by 39k • written 5.4 years ago by ▴ 10
4
votes
1
reply
1.7k
views
Tutorial: One of the easy way to achieve read count and RPKM file
RNA-Seq
updated 22 days ago by 39k • written 5.8 years ago by ▴ 40
15
votes
1
reply
6.4k
views
Tutorial: A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl SAM blast BED
updated 20 days ago by 39k • written 5.6 years ago by ★ 3.0k
1
vote
0
replies
1.8k
views
Tutorial: How to display Agilent CGH array in IGV
IGV CGH
updated 20 days ago by 39k • written 5.5 years ago by ★ 2.4k
0
votes
0
replies
2.6k
views
Tutorial: Autocorrelation With Breusch Godfrey Serial Correlation LM Test R Commander
LM-Test R Autocorrelation Breusch-Godfrey
updated 20 days ago by 39k • written 5.5 years ago by ▴ 10
1
vote
0
replies
1.3k
views
Tutorial: Fall 2017 Introduction to Human Genomics for Clinical Informaticists
genome
updated 19 days ago by 39k • written 5.4 years ago by ▴ 90
0
votes
0
replies
111
views
Tutorial: How to start disease research quickly and easily?
proteins pathways disease research-design genes
1 day ago by Coremine Medical ▴ 10
3
votes
0
replies
2.1k
views
Tutorial: Deep Learning for Cancer Immunotherapy
keras tensorflow
updated 19 days ago by 39k • written 5.4 years ago by 21k
0
votes
0
replies
1.1k
views
Tutorial: In the cloud - Guide to running VerifyBamID to estimate DNA sample contamination
sequence cloud dna sequencing
updated 14 days ago by 39k • written 4.8 years ago by • 0
2
votes
0
replies
6.5k
views
Tutorial: How to - Install Python packages in a virtual environment (virtualenv)
ubuntu cutadapt virtualenv python windows
updated 20 days ago by 39k • written 5.5 years ago by ▴ 310
0
votes
0
replies
1.4k
views
Tutorial: PLS SEM (Partial Least Square Sructural Equation Modeling) Analysis WarpPLS 6
R
updated 20 days ago by 39k • written 5.3 years ago by ▴ 10
0
votes
0
replies
1.2k
views
Tutorial: Data Panel In R Commander
R
updated 20 days ago by 39k • written 5.5 years ago by ▴ 10
4
votes
0
replies
2.1k
views
Tutorial: Accurate prediction of active enhancers using PARE
ChIP-Seq histone-modification enhancer
updated 27 days ago by 39k • written 6.1 years ago by ▴ 100
0
votes
0
replies
3.4k
views
Tutorial: SFA (Stochastic Frontier Analysis) STATA 14
R
updated 20 days ago by 39k • written 5.3 years ago by ▴ 10
2
votes
0
replies
1.2k
views
Tutorial: Free Book : Computational Biology of a cell signalling pathway using R
cell-signalling R Computational-Biology
updated 7 days ago by 39k • written 17 months ago by ▴ 20
2
votes
0
replies
1.2k
views
Tutorial: Principal Component Analysis (PCA ON T-BIOINFO)
RNA-Seq next-gen
updated 14 days ago by 39k • written 5.0 years ago by ▴ 340
59 results • Page 1 of 2
Recent Votes
Answer: Saving results from yeastgenome.org blastp search
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data.
Answer: Saving results from yeastgenome.org blastp search
Comment: snps from empty well, Illumina Sequencing
Extract sequences from a fastq file by a list of IDs
Answer: Extract sequences from a fastq file by a list of IDs
Answer: Differences in GTF files hg19 and hg38
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Popular Question to Payal ▴ 140
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Recent Replies
Comment: VCF file CSQ flag by Payal ▴ 140
Its a gvcf file #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S101 S102 S103 S104 S105
Comment: CellRanger problem by GenoMax 130k
And how much memory do you have assigned for this job? Likely you do not have enough memory for this process.
Comment: VCF file CSQ flag by Ram 39k
> a g.VCF file A `.vcf` file or a `gvcf` file?
Comment: CellRanger problem by Ram 39k
What is the cellranger command you're using?
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data. by Yeeshouw • 0
I see, I believe I was running an older version or have missed the option, I have updated to v2.10.5 and can see this option now. Thank you…
Answer: Saving results from yeastgenome.org blastp search by GenoMax 130k
Looks like yeastgenome site does not provide a way to export or save the results in any other format. You could do the search over at NCBI …
Answer: Differences in GTF files hg19 and hg38 by GenoMax 130k
Not sure where you got your GTF for GRCh38 from but [**one from GENCODE**][1] has the level info you are looking for. chr1 HAVANA…
Comment: CHiP-Seq Questions by B.N. • 0
Thank you for the suggestions Dr. Stark.
Comment: Diff Bind Questions by B.N. • 0
Thank you so much for the insight Dr. Stark!
Comment: Is PanCan data microarray or rna-seq by GenoMax 130k
This particular example ("GeneChip") is an array. Early TCGA samples may have been done using arrays and later sequenced. Appears to be thi…
Comment: ChatGPT optimized for bioinformatics questions by Sasha ▴ 280
Hoping to add functionality around this. Stay tuned. Big problem for our space that needs to be resolved.
Comment: Is PanCan data microarray or rna-seq by solarchan7 • 0
Hi, so this [paper](https://www.nature.com/articles/s41598-019-45165-4) uses the TCGA dataset and in the supplementary information, it ment…
Comment: counts matrix should be numeric, currently it has mode: character when using a c by Darked89 4.4k
Since the input file is named `normalized.csv` and the values look like floats most likely the counts have been already normalized somehow.
Comment: Embryo transcriptome by Basti ★ 1.6k
https://www.ebi.ac.uk/ena/browser/view/PRJEB11202 https://www.ebi.ac.uk/ena/browser/view/PRJNA153427
Comment: ChatGPT optimized for bioinformatics questions by ATpoint 72k
How is it trained on PubMed/papers? One major drawback of ChatGPT is that it wildly makes up papers that do not even exist but with great c…
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