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Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 9 days ago by 39k • written 7.8 years ago by ★ 4.6k
78
votes
42
replies
29k
views
25 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 25 days ago by 39k • written 9.6 years ago by ★ 7.7k
83
votes
34
replies
16k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 7 days ago by • 0 • written 4.9 years ago by ★ 1.3k
45
votes
28
replies
7.3k
views
9 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
15 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 15 days ago by 39k • written 5.4 years ago by ▴ 310
34
votes
17
replies
15k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning classification
updated 29 days ago by 129k • written 9.5 years ago by 20k
59
votes
15
replies
12k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 8 days ago by 39k • written 4.6 years ago by 16k
17
votes
13
replies
1.7k
views
Tutorial: Screen shots of text (please don't)!
meta
updated 22 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 23 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 17 days ago by 39k • written 5.7 years ago by 85k
14
votes
9
replies
4.2k
views
6 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
aspera ascp
updated 29 days ago by • 0 • written 11 months ago by 72k
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 17 days ago by 39k • written 5.7 years ago by 85k
11
votes
7
replies
7.3k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 14 days ago by 39k • written 2.2 years ago by ▴ 300
39
votes
6
replies
17k
views
Tutorial: Creating chromosome karyotype plot with R and ggplot2
ggplot2 R chromosome karyotype
updated 17 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 16 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 18 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 11 days ago by 39k • written 5.1 years ago by ★ 2.4k
10
votes
4
replies
2.8k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 14 days ago by 39k • written 5.3 years ago by 85k
3
votes
4
replies
3.4k
views
Tutorial: Gene Set Enrichment Analysis on T-BioInfo
gene RNA-Seq
updated 8 days ago by 39k • written 4.6 years ago by ▴ 340
1
vote
4
replies
3.0k
views
Tutorial: Applying machine learning to NGS transcriptomic data
next-gen RNA-Seq
updated 11 days ago by 39k • written 5.1 years ago by ▴ 340
2
votes
3
replies
2.4k
views
Tutorial: It's about the journey, and not the destination
R network
updated 22 days ago by 39k • written 6.2 years ago by ★ 1.2k
3
votes
3
replies
7.9k
views
Tutorial: High Speed Downloading of SRA, SAM and Fastq Files
fastq sam Aspera-Connect sra
updated 15 days ago by 39k • written 5.4 years ago by ▴ 100
5
votes
2
replies
2.8k
views
Tutorial: Get GC Content from UCSC with perl script (mysql)
myql ucsc gc-content perl
updated 22 days ago by 39k • written 6.1 years ago by ★ 9.3k
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 21 days ago by 39k • written 6.0 years ago by ★ 1.5k
3
votes
2
replies
2.1k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences Workshops
updated 21 days ago by 39k • written 6.1 years ago by ▴ 100
18
votes
2
replies
5.5k
views
Tutorial: Update kraken databases
database kraken k-mer python
updated 21 days ago by 39k • written 6.1 years ago by 5.2k
20
votes
2
replies
7.2k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 16 days ago by 39k • written 5.5 years ago by ★ 3.4k
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 22 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 22 days ago by 39k • written 6.2 years ago by ▴ 640
2
votes
2
replies
7.8k
views
Tutorial: Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ UMI fastp
updated 16 days ago by 39k • written 5.5 years ago by ★ 2.4k
3
votes
2
replies
3.5k
views
Tutorial: Galaxy Tutorial on ChIP-seq
galaxy ChIP-Seq
updated 22 days ago by 39k • written 6.1 years ago by ▴ 30
7
votes
2
replies
1.7k
views
Tutorial: Introduction to Human Genomics for Clinical Informaticists
genome
updated 17 days ago by 39k • written 5.8 years ago by ▴ 90
10
votes
2
replies
3.4k
views
Tutorial: Graph visualization with igraph in R
Visualization igraph Graph R Network
updated 22 days ago by 39k • written 6.1 years ago by 26k
10
votes
1
reply
7.7k
views
Tutorial: How to select reads with specific flag using samtools
next-gen-sequencing
updated 17 days ago by 39k • written 5.7 years ago by ▴ 110
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 16 days ago by 39k • written 5.6 years ago by ★ 3.0k
0
votes
1
reply
2.8k
views
Tutorial: Accessing sequences using batch entrez
genome
updated 16 days ago by 39k • written 5.6 years ago by • 0
0
votes
1
reply
1.7k
views
Tutorial: Nonparametric Regression STATA 15
STATA-15 Nonparametric-Regression STATA
updated 15 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 17 days ago by 39k • written 5.8 years ago by ▴ 40
7
votes
1
reply
2.0k
views
Tutorial: A gentle introduction to biogo
sequence golang biogo
updated 16 days ago by 39k • written 5.6 years ago by ★ 1.7k
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 21 days ago by 39k • written 6.0 years ago by ★ 1.5k
3
votes
0
replies
2.1k
views
Tutorial: Deep Learning for Cancer Immunotherapy
keras tensorflow
updated 15 days ago by 39k • written 5.3 years ago by 21k
3
votes
0
replies
310
views
Tutorial: How to make a heatmap in R and deep understand it
heatmap r
29 days ago by Ming Tommy Tang ★ 2.9k
2
votes
0
replies
6.5k
views
Tutorial: How to - Install Python packages in a virtual environment (virtualenv)
ubuntu cutadapt virtualenv python windows
updated 15 days ago by 39k • written 5.5 years ago by ▴ 310
1
vote
0
replies
1.5k
views
Tutorial: Using Subversion to update /devel branch of Bioconductor package
bioconductor subversion
updated 18 days ago by 39k • written 5.8 years ago by ▴ 350
0
votes
0
replies
1.2k
views
Tutorial: Data Panel In R Commander
R
updated 15 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 22 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 15 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 2 days ago by 39k • written 17 months ago by ▴ 20
0
votes
0
replies
2.0k
views
Tutorial: Transforming (Transformation) Data LN, Log, SQRT In R Commander
R
updated 15 days ago by 39k • written 5.4 years ago by ▴ 10
2
votes
0
replies
1.2k
views
Tutorial: Principal Component Analysis (PCA ON T-BIOINFO)
RNA-Seq next-gen
updated 9 days ago by 39k • written 5.0 years ago by ▴ 340
61 results • Page 1 of 2
Recent Votes
Comment: Low mapping percentage
Comment: Low mapping percentage
A: genomicranges outside sequence bounds
A: how can i download human ribosomal reference ?
Bayesian network for biological data using bnlearn
Comment: What does canonical transcript mean in the context of VEP
Answer: What does canonical transcript mean in the context of VEP
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Recent Replies
Comment: Low mapping percentage by Sib ▴ 40
Thank you for the reply. If there is not much I can do about the contamination at this stage, what is the benefit of knowing the source of…
Answer: integrate single cell RNA sequencing data by Hamid Ghaedi 2.9k
There are different approaches that you may choose to deal with batch correction. Harmony is one of those approaches that has been shown to…
Comment: What does canonical transcript mean in the context of VEP by Vincent Laufer ★ 2.9k
@curious - The only thing I have to add to @yokofakun 's precise answer is that, while you are considering and reading about Ensembl canoni…
Comment: Help with running ATAC using Encode pipeline by Chris ▴ 100
Thank you for the instruction! I see the beside json file we also have input file which I am confused. Because we have already defined the …
Comment: Comparing loci across catalogs by rycro_c • 0
Hi @Austin, Did you ever figure this out?
Comment: Low mapping percentage by Dave Carlson ★ 1.3k
I've been faced with similar issues in the past. Both option 1 and 2 seem useful. You can also treat your data as accidental metagenomic …
Comment: How to sort gff3 according to chromosome order? by Pierre Lindenbaum 154k
-s, --stable stabilize sort by disabling last-resort comparison
Comment: Low mapping percentage by GenoMax 129k
If you do have contamination (either from rRNA of same species or from true contaminant(s)) there is not much you can do about that at this…
Comment: Optimum setting for local blastp for ~10K sequences by GenoMax 129k
> Running the same sequence on the blast web server took 10 seconds Don't try to compare anything local with NCBI's web blast infrastruct…
Comment: how to Construct a Newick tree file from five large fasta files by Joe 21k
Yes, I know - but that doesn't answer the question. **What *kind* of phylogenetic tree?**
Comment: Optimum setting for local blastp for ~10K sequences by sodiumnitrate ▴ 20
Thank you for the explanation! I managed to get diamond to work, but I'm having trouble getting it to run faster than blast. For a single t…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig by GenoMax 129k
That is the question @Vincent answer poses since it seems to correspond to something different. You can also create an issue on https://gi…
Answer: How to sort gff3 according to chromosome order? by GenoMax 129k
Please use `AGAT`: https://agat.readthedocs.io/en/latest/topological-sorting-of-gff-features.html
Comment: convert data frame with character column to data frame with integer column by atemedorri137798 • 0
dear @Basti : As you said in order to clarify my issue I edit question box with give an example. I will be grateful if you take a look at …
Comment: How to sort gff3 according to chromosome order? by Ram 39k
Those are your options with the `sort` utility - you can either keep the existing order or re-order by coordinate. If you're looking for a …
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