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412 results • Page 6 of 9
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Tutorial: Get GC Content from UCSC with perl script (mysql)
myql ucsc gc-content perl
updated 12 months ago by 43k • written 7.1 years ago by ★ 9.4k
5
votes
0
replies
2.2k
views
Tutorial: Installing multiprocessor-capable MEME to work with a Slurm job scheduler environment
slurm meme parallel
updated 12 months ago by 43k • written 6.7 years ago by 35k
9
votes
9
replies
4.2k
views
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
reference-coverage ngs
updated 12 months ago by 43k • written 6.7 years ago by 88k
12
votes
4
replies
2.2k
views
Tutorial: Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR DESeq2
updated 13 months ago by 43k • written 6.7 years ago by ▴ 590
11
votes
7
replies
14k
views
Tutorial: Removing rows with duplicate values based on 1 or more key values - linux awk
awk linux bash
updated 12 months ago by 43k • written 6.7 years ago by 88k
7
votes
2
replies
1.9k
views
Tutorial: Introduction to Human Genomics for Clinical Informaticists
genome
updated 12 months ago by 43k • written 6.7 years ago by ▴ 90
4
votes
1
reply
1.9k
views
Tutorial: One of the easy way to achieve read count and RPKM file
RNA-Seq
updated 12 months ago by 43k • written 6.8 years ago by ▴ 40
1
vote
0
replies
1.7k
views
Tutorial: Using Subversion to update /devel branch of Bioconductor package
bioconductor subversion
updated 12 months ago by 43k • written 6.8 years ago by ▴ 350
12
votes
11
replies
7.6k
views
Tutorial: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI Bioproject SRA BioSample
updated 12 months ago by 43k • written 7.2 years ago by ★ 2.4k
9
votes
5
replies
2.3k
views
Tutorial: What is new in samtools release 1.5 [Solstice Release] (21st June 2017)
samtools
updated 12 months ago by 43k • written 6.8 years ago by 100k
26
votes
15
replies
8.9k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
course training mooc
updated 14 months ago by 43k • written 11.3 years ago by 9.7k
54
votes
5
replies
15k
views
6 follow
Tutorial: Machine Learning For Cancer Classification - Part 4 - Plotting A Kaplan-Meier Curve For Survival Analysis
r
updated 19 months ago by 43k • written 10.5 years ago by ★ 1.2k
3
votes
1
reply
2.3k
views
Tutorial: Convert bam files to fastq in numbers as indicated in samtools flagstat stats.
samtools bam alignment fastq sequence
updated 12 months ago by 43k • written 6.9 years ago by ★ 1.6k
6
votes
2
replies
4.2k
views
Tutorial: GATK method for filtering vcf lines using GT values at all or multisample level.
genome vcf genotype variant-filtration
updated 12 months ago by 43k • written 7.0 years ago by ★ 1.6k
2
votes
6
replies
3.2k
views
Tutorial: Rembrandt Glioma Data Analysis (PART I) - Are Gender specific genes related to cancer ?
gene R Rembrandt
updated 13 months ago by 43k • written 7.8 years ago by ▴ 140
7
votes
2
replies
12k
views
Tutorial: Howto use NCBI programs behind a HTTP proxy
blast-plus HTTP-proxy SRA-toolkit
updated 22 months ago by 43k • written 8.2 years ago by ★ 1.8k
12
votes
6
replies
5.0k
views
Tutorial: sharing some naive codes for microarray normalization in R with whom are too new in R alike me
R
updated 22 months ago by 43k • written 8.3 years ago by ★ 4.3k
4
votes
0
replies
2.3k
views
Tutorial: Accurate prediction of active enhancers using PARE
ChIP-Seq histone-modification enhancer
updated 12 months ago by 43k • written 7.1 years ago by ▴ 100
3
votes
2
replies
3.9k
views
Tutorial: Galaxy Tutorial on ChIP-seq
galaxy ChIP-Seq
updated 12 months ago by 43k • written 7.1 years ago by ▴ 30
10
votes
2
replies
3.7k
views
Tutorial: Graph visualization with igraph in R
Visualization igraph Graph R Network
updated 12 months ago by 43k • written 7.1 years ago by 27k
20
votes
2
replies
3.4k
views
Tutorial: Beginner's Handbook to Next Generation Sequencing
NGS
updated 12 months ago by 43k • written 7.1 years ago by ▴ 650
2
votes
3
replies
2.7k
views
Tutorial: It's about the journey, and not the destination
R network
updated 12 months ago by 43k • written 7.1 years ago by ★ 1.2k
18
votes
13
replies
2.2k
views
Tutorial: Screen shots of text (please don't)!
meta
updated 12 months ago by 43k • written 7.1 years ago by 54k
2
votes
3
replies
2.0k
views
Tutorial: Help demonstrate reproducibility in bioinformatics with the GA4GH's tool execution Challenge
GA4GH Docker CWL Rabix
updated 13 months ago by 43k • written 7.2 years ago by ▴ 20
16
votes
6
replies
6.5k
views
Tutorial: How to make your snakefiles self-documenting
snakemake
updated 13 months ago by 43k • written 7.5 years ago by ★ 1.7k
0
votes
2
replies
5.4k
views
Tutorial: Install AMOS on Ubuntu 13.10
sequencing alignment software-error next-gen
updated 2.5 years ago by 43k • written 9.9 years ago by 9.7k
8
votes
2
replies
6.6k
views
Tutorial: Troubleshooting issues with SURPI pipeline for pathogen identification from complex metagenomic NGS data.
metagenomics clinical-genomics
updated 2.3 years ago by 43k • written 9.5 years ago by 12k
15
votes
2
replies
6.9k
views
Tutorial: Genotype And Snp Calling Review Papers
snp
updated 14 months ago by 43k • written 11.7 years ago by 100k
90
votes
19
replies
32k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray bioconductor expression classification
updated 14 months ago by 43k • written 10.5 years ago by 20k
19
votes
4
replies
8.9k
views
Tutorial: Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 14 months ago by 43k • written 11.2 years ago by 100k
6
votes
11
replies
5.7k
views
6 follow
Tutorial: Add count numbers to headers in a fasta file
genome
updated 15 months ago by 43k • written 7.4 years ago by ▴ 50
15
votes
2
replies
3.1k
views
Tutorial: Introduction to bedtools.
bedtools
updated 14 months ago by 43k • written 9.5 years ago by 12k
0
votes
0
replies
1.4k
views
Tutorial: Webinar: Accelerating skin research by pre-screening of molecules for skin sensitization risk
skin-sensitization chemoinformatics
updated 13 months ago by 43k • written 7.5 years ago by ▴ 10
99
votes
8
replies
29k
views
8 follow
Tutorial: Guide to TCGA data
cancer RNA-Seq clinical TCGA
updated 13 months ago by 43k • written 8.2 years ago by ★ 1.1k
0
votes
0
replies
2.1k
views
Tutorial: PBS setting combination for bismark alignment to BS-seq or RRBS data
pbs bismark
updated 13 months ago by 43k • written 7.5 years ago by ★ 9.4k
0
votes
0
replies
2.1k
views
Tutorial: New GATB-Core Tutorial: learn the Genome Analysis Tool Box... online
next-gen GATB
updated 13 months ago by 43k • written 7.5 years ago by ▴ 140
0
votes
0
replies
1.6k
views
Tutorial: Free Online Course "Code of Life" started today
genome gene sequence
updated 13 months ago by 43k • written 7.5 years ago by • 0
12
votes
5
replies
8.4k
views
Tutorial: How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
updated 13 months ago by 43k • written 8.0 years ago by ★ 9.4k
30
votes
14
replies
16k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
genome-music linux smg
updated 14 months ago by 43k • written 11.3 years ago by 6.1k
1
vote
1
reply
1.8k
views
Tutorial: Live webinar: Implications of Next Generation Sequencing in Molecular Diagnosis of Cancer on 28 Sep 2016
alignment sequencing genome SNP
updated 13 months ago by 43k • written 7.7 years ago by ▴ 70
142
votes
21
replies
30k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 2.0 years ago by 43k • written 9.4 years ago by ★ 1.6k
20
votes
4
replies
8.6k
views
Tutorial: DE analysis by edgeR
RNA-Seq R edgeR
updated 13 months ago by 43k • written 7.7 years ago by ★ 4.3k
7
votes
2
replies
1.7k
views
Tutorial: A tale of two heatmap function
clustering heatmap
updated 13 months ago by 43k • written 7.7 years ago by ★ 3.9k
14
votes
0
replies
9.6k
views
Tutorial: How to generate PCA plot and heatmaps in R
heatmap PCA RNA-Seq R
updated 13 months ago by 43k • written 7.7 years ago by ★ 3.9k
0
votes
2
replies
2.4k
views
Tutorial: COURSE: NGS variant analysis and interpretation for translational research
CNIO course translational
updated 13 months ago by 43k • written 7.7 years ago by ▴ 190
1
vote
3
replies
3.2k
views
Tutorial: resolving error of sspace_standard
software-error Assembly
updated 13 months ago by 43k • written 7.7 years ago by ▴ 300
15
votes
5
replies
16k
views
Tutorial: How to create a mutation lolliplot with GenVisR
bioconductor graphics R genvisr
updated 13 months ago by 43k • written 7.9 years ago by 20k
3
votes
0
replies
1.9k
views
Tutorial: Project-based bioinformatics workshops online
ChIP-Seq RNA-Seq genome gene
updated 13 months ago by 43k • written 7.8 years ago by ▴ 340
11
votes
3
replies
1.4k
views
Tutorial: Creating great documentation for bioinformatics software
Software-Documentation
updated 13 months ago by 43k • written 7.8 years ago by 7.1k
0
votes
0
replies
2.5k
views
Tutorial: Rembrandt Glioma Data Analysis (PART II) - Are Gender specific genes related to cancer ?
gene R Rembrandt
updated 13 months ago by 43k • written 7.8 years ago by ▴ 140
412 results • Page 6 of 9
Recent Votes
The Biostar Herald for Monday, May 13, 2024
Answer: Finding variants within a subset of a BAM file
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
Answer: Help with IGV abbreviation
Split multiallelic SNPs to biallelic from vcf
Filtering multi-allelic sites in VCF files
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Recent Replies
Comment: Overlapping Ranges within Granges object by ntsopoul ▴ 60
does this work with a single .bed file?
Comment: Finding variants within a subset of a BAM file by ramiro.barrantes • 0
Actually, I found a solution in downloading "bam slices" from TCGA ([https://docs.gdc.cancer.gov/API/Users_Guide/BAM_Slicing/][1]) , which …
Comment: Overlapping Ranges within Granges object by ntsopoul ▴ 60
![enter image description here][1]Here is some representative data and an image in igv of one gene. I have loaded the .bed file in igv. As …
Answer: RNAseq RNA content by ntsopoul ▴ 60
I guess he/she means raw RNA. Roughly 2% of all RNA is mRNA the rest is rRNA. I think the first thing you need to figure out is with which …
Comment: RNAseq RNA content by ATpoint 82k
What is "row RNA"?
Comment: Overlapping Ranges within Granges object by ATpoint 82k
I would probably collapse overlapping regions with `reduce` to create the second GRanges. Can you add some representative data? Using dput?
Comment: Overlapping Ranges within Granges object by ntsopoul ▴ 60
I have one Granges object and not two. Every IRanges entry is the critical region of the gRNA. Can this still work?
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments? by J. ▴ 40
FYI if you also have this problem, this seems to be a pretty good solution: https://github.com/harvardinformatics/degenotate
Comment: Biomart issue, why so few 3'utrs? by GenoMax 142k
AFAIK "MANE" project is only for human protein-coding genes. One potential explanation. Out of the 2000 ID's only 125 may be MANE. https:…
Answer: Biomart issue, why so few 3'utrs? by i.sudbery 19k
The MANE-select transcripts are pairs of identically annotated transcripts in ReqSeq and Ensembl. The 3' UTR is the region where otherwise …
Comment: sci-RNA-seq by ATpoint 82k
Please understand that this impossibly can be answered without any code or plots, or details in general. "Hey my car does not start, it mak…
Comment: Biomart issue, why so few 3'utrs? by i.sudbery 19k
Which species is this?
Comment: How to access GWAVA software of data by GenoMax 142k
Please email the author (grsr at ebi.ac.uk) and let them know that the link above is not available.
Comment: CNVKIT - unable to produce scatter and diagram pdfs by Anitha • 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Comment: CNVkit for somatic copy number detection by Anitha • 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
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