Limit : this month
all time today this week this month this year
58 results • Page 1 of 2
Sort: replies
Rank Views Votes Replies
238
votes
176
replies
85k
views
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
0
votes
1
reply
2.8k
views
Tutorial: Accessing sequences using batch entrez
genome
updated 18 days ago by 39k • written 5.6 years ago by • 0
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
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
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
0
votes
1
reply
1.7k
views
Tutorial: Nonparametric Regression STATA 15
STATA-15 Nonparametric-Regression STATA
updated 17 days ago by 39k • written 5.4 years ago by ▴ 10
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
0
votes
0
replies
7.6k
views
Tutorial: Multicollinearity VIF (Variance Inflation Factor) Analysis in Panel data EVIEWS 9
R eviews
updated 17 days ago by 39k • written 5.4 years ago by ▴ 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
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 11 days ago by 39k • written 4.8 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 17 days ago by 39k • written 5.5 years ago by ▴ 10
2
votes
0
replies
6.5k
views
Tutorial: How to - Install Python packages in a virtual environment (virtualenv)
ubuntu cutadapt virtualenv python windows
updated 17 days ago by 39k • written 5.5 years ago by ▴ 310
0
votes
0
replies
2.0k
views
Tutorial: Transforming (Transformation) Data LN, Log, SQRT In R Commander
R
updated 17 days ago by 39k • written 5.4 years ago by ▴ 10
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
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
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
0
votes
0
replies
1.2k
views
Tutorial: Data Panel In R Commander
R
updated 17 days ago by 39k • written 5.5 years ago by ▴ 10
0
votes
0
replies
3.4k
views
Tutorial: SFA (Stochastic Frontier Analysis) STATA 14
R
updated 17 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 4 days ago by 39k • written 17 months ago by ▴ 20
58 results • Page 1 of 2
Recent Votes
Answer: How To Predict Pseudogenes In A Genome
A: How To Predict Pseudogenes In A Genome
A: How To Predict Pseudogenes In A Genome
A: How To Predict Pseudogenes In A Genome
How To Predict Pseudogenes In A Genome
C: parsing fasta file
SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
Recent Locations • All
France, just now
Oxford, UK, 2 minutes ago
University Park, USA, 2 minutes ago
Latent Space, 2 minutes ago
United States, 3 minutes ago
United States, 3 minutes ago
Italy, 3 minutes ago
Recent Awards • All
Teacher to antonioggsousa 2.8k
Teacher to Kevin Blighe 85k
Popular Question to bioinfo_ga ▴ 50
Popular Question to english.server ▴ 290
Teacher to Pierre Lindenbaum 154k
Voter to pilargmarch ▴ 100
Popular Question to anna ▴ 10
Recent Replies
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…
Comment: Getting same value for start and end position, "DNA methylation" by ATpoint 72k
That's a comment, not an answer, please use `ADD COMMENT`.
Comment: Getting same value for start and end position, "DNA methylation" by bioinfo_ga ▴ 50
Are you working on bisulphite kind of data or chipseq ????
Answer: How to calculate TPM from featureCounts output by bioinfo_ga ▴ 50
hi , You can use a python package rnanorm [https://pypi.org/project/rnanorm/]. The input required are your read count values from feature …
Comment: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by by biofalconch ▴ 580
Hey, if you arelady have the barcodes, you could use samtools `samtools view -h -b -f CB:Z:TAAGAGATCCTATGTT > TAAGAGATCCTATGTT.bam` Hope…
Answer: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by by biofalconch ▴ 580
Here is a code that should work, but just like everyone else in the comments I'm a little confused why would you need to separate them: …
Comment: Make a BedGraph file by kirillkirilenko ▴ 10
It works, thank you!
Comment: CNNScoreVariants Error by Pierre Lindenbaum 154k
check you have a complete environment for GATK , including the python module "keras". https://gatk.broadinstitute.org/hc/en-us/articles/360…
Comment: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by by Cathal • 0
Did you have any luck in splitting the BAM file based on the 10x cell barcode? I would like to split a BAM file based to only include 5 spe…
Answer: Getting same value for start and end position, "DNA methylation" by ATpoint 72k
genomation is based on GenomicRanges which uses 1-based coordinates. https://www.biostars.org/p/84686/ Since a single CpG has a length o…
Traffic: 2476 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6