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238
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176
replies
85k
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73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 11 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 9 days ago by • 0 • written 5.0 years ago by ★ 1.3k
78
votes
42
replies
29k
views
25 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 27 days ago by 39k • written 9.6 years ago by ★ 7.7k
59
votes
15
replies
12k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 10 days ago by 39k • written 4.7 years ago by 16k
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
17 days ago by Ram 39k
39
votes
6
replies
17k
views
Tutorial: Creating chromosome karyotype plot with R and ggplot2
ggplot2 R chromosome karyotype
updated 19 days ago by 39k • written 5.8 years ago by ★ 3.3k
20
votes
2
replies
7.2k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 18 days ago by 39k • written 5.5 years ago by ★ 3.4k
19
votes
2
replies
3.1k
views
Tutorial: Beginner's Handbook to Next Generation Sequencing
NGS
updated 24 days ago by 39k • written 6.2 years ago by ▴ 640
18
votes
2
replies
5.5k
views
Tutorial: Update kraken databases
database kraken k-mer python
updated 23 days ago by 39k • written 6.1 years ago by 5.2k
17
votes
13
replies
1.7k
views
Tutorial: Screen shots of text (please don't)!
meta
updated 24 days ago by 39k • written 6.2 years ago by 52k
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 18 days ago by 39k • written 5.6 years ago by ★ 3.0k
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 25 days ago by 39k • written 6.2 years ago by ★ 2.4k
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 16 days ago by 39k • written 2.3 years ago by ▴ 300
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 19 days ago by 39k • written 5.7 years ago by 85k
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 24 days ago by 39k • written 6.2 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 19 days ago by 39k • written 5.7 years ago by ▴ 110
10
votes
2
replies
3.4k
views
Tutorial: Graph visualization with igraph in R
Visualization igraph Graph R Network
updated 24 days ago by 39k • written 6.2 years ago by 26k
10
votes
4
replies
2.9k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 16 days ago by 39k • written 5.3 years ago by 85k
9
votes
9
replies
3.7k
views
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
reference-coverage ngs
updated 19 days ago by 39k • written 5.7 years ago by 85k
9
votes
23
replies
8.6k
views
7 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 17 days ago by 39k • written 5.4 years ago by ▴ 310
9
votes
5
replies
2.0k
views
Tutorial: What is new in samtools release 1.5 [Solstice Release] (21st June 2017)
samtools
updated 20 days ago by 39k • written 5.9 years ago by 98k
7
votes
2
replies
1.7k
views
Tutorial: Introduction to Human Genomics for Clinical Informaticists
genome
updated 19 days ago by 39k • written 5.8 years ago by ▴ 90
7
votes
1
reply
2.0k
views
Tutorial: A gentle introduction to biogo
sequence golang biogo
updated 18 days ago by 39k • written 5.6 years ago by ★ 1.7k
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 23 days ago by 39k • written 6.0 years ago by ★ 1.5k
5
votes
5
replies
6.1k
views
Tutorial: use firehose_get to download TCGA data
tcga RNA-Seq
updated 18 days ago by 39k • written 5.6 years ago by ▴ 130
5
votes
2
replies
2.8k
views
Tutorial: Get GC Content from UCSC with perl script (mysql)
myql ucsc gc-content perl
updated 24 days ago by 39k • written 6.1 years ago by ★ 9.3k
5
votes
0
replies
2.0k
views
Tutorial: Installing multiprocessor-capable MEME to work with a Slurm job scheduler environment
slurm meme parallel
updated 19 days ago by 39k • written 5.7 years ago by 35k
4
votes
1
reply
1.7k
views
Tutorial: One of the easy way to achieve read count and RPKM file
RNA-Seq
updated 19 days ago by 39k • written 5.8 years ago by ▴ 40
4
votes
0
replies
2.1k
views
Tutorial: Accurate prediction of active enhancers using PARE
ChIP-Seq histone-modification enhancer
updated 24 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 23 days ago by 39k • written 6.0 years ago by ★ 1.5k
3
votes
4
replies
3.4k
views
Tutorial: Gene Set Enrichment Analysis on T-BioInfo
gene RNA-Seq
updated 10 days ago by 39k • written 4.6 years ago by ▴ 340
3
votes
3
replies
7.9k
views
Tutorial: High Speed Downloading of SRA, SAM and Fastq Files
fastq sam Aspera-Connect sra
updated 17 days ago by 39k • written 5.4 years ago by ▴ 100
3
votes
0
replies
2.1k
views
Tutorial: Deep Learning for Cancer Immunotherapy
keras tensorflow
updated 17 days ago by 39k • written 5.3 years ago by 21k
3
votes
2
replies
2.1k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences Workshops
updated 23 days ago by 39k • written 6.1 years ago by ▴ 100
3
votes
2
replies
3.5k
views
Tutorial: Galaxy Tutorial on ChIP-seq
galaxy ChIP-Seq
updated 24 days ago by 39k • written 6.2 years ago by ▴ 30
3
votes
4
replies
4.0k
views
Tutorial: gencore: a tool to reduce sequencing noises by generating consensus reads
consensus OpenGene sequencing-noise
updated 13 days ago by 39k • written 5.1 years ago by ★ 2.4k
2
votes
0
replies
1.4k
views
Tutorial: Webinar: Extracting research evidence from publications
text-mining ontology pubmed
updated 16 days ago by 39k • written 5.3 years ago by ▴ 60
2
votes
0
replies
6.5k
views
Tutorial: How to - Install Python packages in a virtual environment (virtualenv)
ubuntu cutadapt virtualenv python windows
updated 18 days ago by 39k • written 5.5 years ago by ▴ 310
2
votes
2
replies
7.8k
views
Tutorial: Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ UMI fastp
updated 18 days ago by 39k • written 5.5 years ago by ★ 2.4k
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 4 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 11 days ago by 39k • written 5.0 years ago by ▴ 340
2
votes
3
replies
2.4k
views
Tutorial: It's about the journey, and not the destination
R network
updated 24 days ago by 39k • written 6.2 years ago by ★ 1.2k
1
vote
0
replies
22
views
Tutorial: Get a list of genes associated with a drug in 1 min
and drugs targets drug genes
1 hour ago by john ▴ 10
1
vote
0
replies
1.8k
views
Tutorial: How to display Agilent CGH array in IGV
IGV CGH
updated 18 days ago by 39k • written 5.5 years ago by ★ 2.4k
1
vote
4
replies
3.0k
views
Tutorial: Applying machine learning to NGS transcriptomic data
next-gen RNA-Seq
updated 13 days ago by 39k • written 5.1 years ago by ▴ 340
1
vote
0
replies
1.5k
views
Tutorial: Using Subversion to update /devel branch of Bioconductor package
bioconductor subversion
updated 20 days ago by 39k • written 5.8 years ago by ▴ 350
1
vote
0
replies
1.3k
views
Tutorial: Fall 2017 Introduction to Human Genomics for Clinical Informaticists
genome
updated 17 days ago by 39k • written 5.4 years ago by ▴ 90
0
votes
0
replies
3.4k
views
Tutorial: SFA (Stochastic Frontier Analysis) STATA 14
R
updated 18 days ago by 39k • written 5.3 years ago by ▴ 10
0
votes
0
replies
1.4k
views
Tutorial: PLS SEM (Partial Least Square Sructural Equation Modeling) Analysis WarpPLS 6
R
updated 18 days ago by 39k • written 5.3 years ago by ▴ 10
0
votes
0
replies
7.6k
views
Tutorial: Multicollinearity VIF (Variance Inflation Factor) Analysis in Panel data EVIEWS 9
R eviews
updated 18 days ago by 39k • written 5.4 years ago by ▴ 10
59 results • Page 1 of 2
Recent Votes
Answer: I need help with a blast command, please help
Answer: I need help with a blast command, please help
Answer: NCBI API, Perl
Get a list of genes associated with a drug in 1 min
Answer: Getting species names and taxa id from assembly accession number
Pseudogenes-Can we use them?
Comment: If RNA-seq includes miRNA genes then why are there miRNA specific pipelines?
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Recent Replies
Comment: I need help with a blast command, please help by neto.pvp • 0
Thank you very much!! I'm new to this subject and I believe your answer gave me a great idea of where to go next, thanks again!!
Answer: NCBI API, Perl by GenoMax 129k
You are likely best served by using `NCBI datasets` ([**LINK**][1]) or `EntrezDirect` ([**LINK**][2]) command line tools. If you want to …
Comment: Obtain a --gene-trans-map file after rnaSPAdes by GenoMax 129k
You could try to create one: https://groups.google.com/g/trinityrnaseq-users/c/qPbWnLl4iY0 While this is from an unrelated software the so…
Comment: CNNScoreVariants Error by Pierre Lindenbaum 154k
that is another question
Comment: Difference between USCS exon coordinates and ensembl by amy__ ▴ 50
Hi @atpoint, I went to http://genome.ucsc.edu/cgi-bin/hgTables and did: 1. ![enter image description here][1] then: 2. ![enter image…
Comment: should non-protein-coding rna(e.g. lncRNA) be removed in RNA-Seq differential ex by Kermit ▴ 80
See also: https://www.biostars.org/p/9535550/#9536086
Answer: Getting species names and taxa id from assembly accession number by MirianT_NCBI ▴ 590
Hi, As an alternative, you could use [NCBI Datasets][1] for this task. NCBI Datasets allows users to retrieve metadata reports in JSON or…
Comment: Optimum setting for local blastp for ~10K sequences by sodiumnitrate ▴ 20
Thank you for the info! It turned out that running all 10k at once is actually faster than running one or two at a time!
Answer: Installation of PPFinder by GenoMax 129k
Since the software is still [**listed on the Brent lab**][1] website your best bet would be to email the investigator and ask that they fix…
Comment: How to calculate TPM from featureCounts output by rpolicastro 12k
If you want to go that route, yes.
Comment: Difference between USCS exon coordinates and ensembl by ATpoint 72k
What did you download from UCSC? 1-off usually means one file is zero-based and the other 1-based. BED files from UCSC are 0-based, Ensembl…
Comment: Alignment of case vs. control from different origin by sativus • 0
Thank you kindly for the explanation, it is highly appreciated. I suppose i was a bit confused as you quite often see people validating the…
Answer: Gene enrichment analysis by nux ▴ 10
Hello. For this you have to select 'hyper' as your method and then provide a complete list of genes which both include the candidate and no…
Comment: CNNScoreVariants Error by bestone ▴ 10
Thank you for replying I updated it worked but it gives another Error A USER ERROR has occurred: Invalid argument ' -V'.
Comment: Impute haplotypes (ImputePipelinePlugin) execution error - PHG by jrodrigu • 0
Thank you so much. I made the suggested changes. However, I still have the same problem. Please check the new log file. https://github.c…
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