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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 14 days ago by 39k • written 7.8 years ago by ★ 4.6k
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
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
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
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
9
votes
23
replies
8.6k
views
7 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 20 days ago by 39k • written 5.4 years ago by ▴ 310
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
2
replies
7.9k
views
Tutorial: Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ UMI fastp
updated 21 days ago by 39k • written 5.5 years ago by ★ 2.4k
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
0
replies
7.6k
views
Tutorial: Multicollinearity VIF (Variance Inflation Factor) Analysis in Panel data EVIEWS 9
R eviews
updated 20 days ago by 39k • written 5.4 years ago by ▴ 10
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
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
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
20
votes
2
replies
7.2k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 21 days ago by 39k • written 5.5 years ago by ★ 3.4k
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
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
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 21 days ago by 39k • written 5.6 years ago by ★ 3.0k
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
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
3
votes
4
replies
4.0k
views
Tutorial: gencore: a tool to reduce sequencing noises by generating consensus reads
consensus OpenGene sequencing-noise
updated 16 days ago by 39k • written 5.1 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
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
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
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
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
0
votes
0
replies
3.4k
views
Tutorial: Park Test for Heteroskedasticity In R Commander
R Park-Test
updated 20 days ago by 39k • written 5.4 years ago by ▴ 10
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
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
1
vote
4
replies
3.0k
views
Tutorial: Applying machine learning to NGS transcriptomic data
next-gen RNA-Seq
updated 16 days ago by 39k • written 5.1 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
0
votes
0
replies
2.8k
views
Tutorial: Normality Test For JB (Jarque Bera) Test R Commander
Jarque-Bera-Test R-Commander
updated 20 days ago by 39k • written 5.5 years ago by ▴ 10
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
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
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
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
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
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
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
3
votes
0
replies
2.1k
views
Tutorial: Deep Learning for Cancer Immunotherapy
keras tensorflow
updated 20 days ago by 39k • written 5.4 years ago by 21k
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
0
replies
2.0k
views
Tutorial: Transforming (Transformation) Data LN, Log, SQRT In R Commander
R
updated 20 days ago by 39k • written 5.4 years ago by ▴ 10
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
5
votes
0
replies
2.0k
views
Tutorial: Installing multiprocessor-capable MEME to work with a Slurm job scheduler environment
slurm meme parallel
updated 22 days ago by 39k • written 5.7 years ago by 35k
1
vote
0
replies
1.8k
views
Tutorial: How to display Agilent CGH array in IGV
IGV CGH
updated 21 days ago by 39k • written 5.5 years ago by ★ 2.4k
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
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
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
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
1
vote
0
replies
1.5k
views
Tutorial: Using Subversion to update /devel branch of Bioconductor package
bioconductor subversion
updated 23 days ago by 39k • written 5.8 years ago by ▴ 350
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
59 results • Page 1 of 2
Recent Votes
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
A: Mouse promoter regions
Answer: How to get information about promoter from bulk-RNAseq?
A: Extracting Flanking Regions across TSS using R scripts
A: Mouse promoter regions
A: Finding zebrafish promoters ENSEMBL
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Recent Replies
Comment: pal2nal -nogap -nomismatch options not working by Marie • 0
Hi, did you end up solving this? I am running into the same issue. Marie
Comment: How to get information about promoter from bulk-RNAseq? by camillab. ▴ 130
and what about enhancer? is it possible to do it from a bulk-RNAseq?
Comment: How to get information about promoter from bulk-RNAseq? by camillab. ▴ 130
yes! clearly the terminology on my side needs to improved!
Comment: How to get information about promoter from bulk-RNAseq? by rpolicastro 12k
Generally speaking, most promoters only initiate transcription for a single gene, with a single gene potentially having multiple promoters …
Answer: How to get information about promoter from bulk-RNAseq? by Trivas ★ 1.2k
I'd probably select the genes of interest from your bulk RNA-seq results then use the UCSC table browser to get the sequence upstream of th…
Comment: How to add annotation columns with specific colors to the heatmap? by Ram 39k
Show us your exact code - it is quite easy to tweak colors in ComplexHeatmap with the `col=` argument.
Comment: VCF file CSQ flag by Ram 39k
True, but it's not technically impossible to annotate GVCFs, which is why I did not address that point.
Comment: Creating a local version of Clustered NR database by PeterC_NCBI ▴ 260
@genomax Sorry for the delay in reply. We're still working out the details of what exactly to provide. One idea is to provide just the rep…
Comment: Shannon's Entropy by Sliding Window in R by rohitsatyam102 ▴ 690
Hi Were u able to achieve this?
Comment: Differences in GTF files hg19 and hg38 by GenoMax 130k
Since this is not an answer to the original question do not add it as such. I moved your last comment to the correct spot it should have be…
Comment: VCF file CSQ flag by Pierre Lindenbaum 154k
if your talking about the gvcf produced by HaplotypeCaller with ERC=GVCF, you don't annote g.vcf files , you must first merge the g.vcf.f…
Comment: [python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must b by Ram 39k
https://www.biostars.org/u/127538/ : Please delete this question or it will be deleted by moderators in a few days.
Comment: VCF file CSQ flag by Ram 39k
A gvcf files has blocks for both variant loci and non-variant loci, so you won't see a CSQ for each record, only for those variant loci wit…
Comment: Differences in GTF files hg19 and hg38 by heureuse • 0
Thank you very much. I get it from UCSC.
Comment: [python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must b by Arup Ghosh 3.2k
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