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Limit : this year
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231 results • Page
1 of 5
Sort: Votes
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Views
Votes
Replies
276
votes
39
replies
165k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 7 days ago by
Ram
38k • written 8.6 years ago by
Obi Griffith
20k
275
votes
33
replies
92k
views
25 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 4 weeks ago by
Ram
38k • written 9.4 years ago by
Obi Griffith
20k
238
votes
176
replies
84k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 5 months ago by
Ram
38k • written 7.7 years ago by
TriS
★ 4.6k
194
votes
44
replies
68k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 11 weeks ago by
Ram
38k • written 10.5 years ago by
Obi Griffith
20k
146
votes
35
replies
58k
views
33 follow
Tutorial:
Tools For Metagenomic Data Analysis
metagenomics
next-gen
updated 5 weeks ago by
Ram
38k • written 10.3 years ago by
vijay
★ 1.6k
145
votes
34
replies
51k
views
17 follow
Tutorial:
Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music
cancer
tcga
mutation
maf
updated 5 weeks ago by
Ram
38k • written 10.0 years ago by
Cyriac Kandoth
5.9k
144
votes
69
replies
43k
views
19 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 1 day ago by
k001
▴ 10 • written 5.4 years ago by
Kevin Blighe
85k
142
votes
21
replies
29k
views
12 follow
Tutorial:
A few words for R beginners
Swirl
R
updated 11 months ago by
Ram
38k • written 8.3 years ago by
Parham
★ 1.6k
136
votes
25
replies
75k
views
14 follow
Tutorial:
Piping With Samtools, Bwa And Bedtools
unix
samtools
bwa
bedtools
updated 12 months ago by
Ram
38k • written 10.9 years ago by
Ying W
★ 4.2k
130
votes
123
replies
29k
views
23 follow
Tutorial:
Survival analysis with gene expression
cox
gene-expression
survival-analysis
geo
updated 10 days ago by
krushnach80
★ 1.1k • written 4.5 years ago by
Kevin Blighe
85k
116
votes
66
replies
40k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
fastq-dump
Fastq
ENA
updated 18 days ago by
Ram
38k • written 4.7 years ago by
ATpoint
71k
100
votes
6
replies
22k
views
6 follow
Tutorial:
Creating workflows with snakemake and conda
workflow
snakemake
conda
updated 17 days ago by
Ram
38k • written 4.6 years ago by
finswimmer
16k
99
votes
16
replies
30k
views
18 follow
Tutorial:
Heatmaps in R
heatmap
R
updated 17 days ago by
Ram
38k • written 6.7 years ago by
Jean-Karim Heriche
26k
94
votes
25
replies
31k
views
11 follow
Tutorial:
Fastq Quality Control Shootout
quality
qc
trimming
fastq
updated 5 weeks ago by
Ram
38k • written 10.5 years ago by
Istvan Albert
97k
92
votes
105
replies
34k
views
25 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 18 days ago by
Ram
38k • written 4.6 years ago by
Kevin Blighe
85k
89
votes
19
replies
30k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray
bioconductor
expression
classification
updated 4 weeks ago by
Ram
38k • written 9.4 years ago by
Obi Griffith
20k
83
votes
34
replies
15k
views
21 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
active-subnetwork
enrichment
pathway
R
updated 22 days ago by
Ram
38k • written 4.8 years ago by
egeulgen
★ 1.3k
82
votes
21
replies
15k
views
16 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 22 days ago by
Ram
38k • written 2.5 years ago by
Hamid Ghaedi
2.9k
82
votes
28
replies
28k
views
19 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 7 weeks ago by
Ram
38k • written 7.1 years ago by
Obi Griffith
20k
82
votes
21
replies
71k
views
13 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 6 weeks ago by
cmdcolin
★ 2.9k • written 4.7 years ago by
otwtgin2010
▴ 540
81
votes
8
replies
7.8k
views
6 follow
Tutorial:
Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop
lectures
genomics
training
updated 25 days ago by
Ram
38k • written 8.8 years ago by
Malachi Griffith
19k
80
votes
2
replies
53k
views
Tutorial:
How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 4 weeks ago by
Ram
38k • written 9.8 years ago by
Eric Normandeau
11k
78
votes
41
replies
28k
views
24 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 4 months ago by
Acadia
• 0 • written 9.5 years ago by
Irsan
★ 7.7k
75
votes
70
replies
16k
views
18 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
updated 17 days ago by
Ram
38k • written 5.1 years ago by
Kevin Blighe
85k
74
votes
13
replies
65k
views
10 follow
Tutorial:
Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r
cancer
classification
updated 5 months ago by
Ram
38k • written 9.4 years ago by
Nicholas Spies
★ 1.2k
73
votes
14
replies
14k
views
15 follow
Tutorial:
List Of Bioinformatics Books
books
updated 7 weeks ago by
Ram
38k • written 9.9 years ago by
Medhat
9.5k
72
votes
48
replies
15k
views
15 follow
Tutorial:
For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs
alignment
bwa
updated 5 weeks ago by
Ram
38k • written 10.1 years ago by
lh3
33k
72
votes
60
replies
23k
views
16 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes
PLINK
PCA
VCF
updated 7 weeks ago by
Ram
38k • written 5.6 years ago by
Kevin Blighe
85k
70
votes
5
replies
10k
views
8 follow
Tutorial:
Bioinformatics For Metagenomic Analyses
QC
taxonomy
metagenomics
updated 12 months ago by
Ram
38k • written 9.0 years ago by
umer.zeeshan.ijaz
★ 1.8k
68
votes
26
replies
24k
views
15 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 29 days ago by
Ram
38k • written 9.1 years ago by
Istvan Albert
97k
67
votes
6
replies
24k
views
7 follow
Tutorial:
Rna-Seq Review Papers
RNA-seq
papers
updated 5 weeks ago by
Ram
38k • written 10.6 years ago by
Istvan Albert
97k
65
votes
9
replies
47k
views
7 follow
Tutorial:
Reference Assembly - Mapping Reads To A Reference Genome
reference
samtools
mapping
bwa
updated 7 weeks ago by
Ram
38k • written 9.8 years ago by
Joseph Hughes
★ 3.0k
64
votes
26
replies
11k
views
7 follow
Tutorial:
Parallel processing in R
biocparallel
mclapply
foreach
R
updated 17 days ago by
Ram
38k • written 5.5 years ago by
Kevin Blighe
85k
64
votes
5
replies
6.7k
views
10 follow
Tutorial:
Informatics of RNA-Seq.
next-gen
RNA-Seq
updated 5 months ago by
Ram
38k • written 7.7 years ago by
GouthamAtla
12k
64
votes
26
replies
11k
views
11 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 18 days ago by
Ram
38k • written 4.1 years ago by
finswimmer
16k
60
votes
6
replies
8.9k
views
Tutorial:
Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 4 weeks ago by
Ram
38k • written 9.6 years ago by
Medhat
9.5k
60
votes
2
replies
6.9k
views
Tutorial:
Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 5 weeks ago by
Ram
38k • written 10.6 years ago by
Istvan Albert
97k
60
votes
52
replies
39k
views
23 follow
Tutorial:
Creating Interactive Volcano Plots with R and Plot.ly
plotly
R
volcano-plot
updated 17 days ago by
Ram
38k • written 6.5 years ago by
steve
★ 3.3k
59
votes
43
replies
18k
views
18 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign
pacbio
arrow
smrt-limk
updated 17 days ago by
Ram
38k • written 5.5 years ago by
Rox
★ 1.4k
58
votes
25
replies
36k
views
15 follow
Tutorial:
Protocol To Downlad TCGA Data From GDC
GDC
methylation
TCGA
updated 14 days ago by
Ram
38k • written 6.7 years ago by
Shicheng Guo
★ 9.3k
53
votes
5
replies
14k
views
6 follow
Tutorial:
Machine Learning For Cancer Classification - Part 4 - Plotting A Kaplan-Meier Curve For Survival Analysis
r
updated 6 months ago by
Ram
38k • written 9.3 years ago by
Nicholas Spies
★ 1.2k
51
votes
3
replies
22k
views
Tutorial:
Sam File Format - Lesser Known Tips And Tricks
sam
updated 5 weeks ago by
Ram
38k • written 10.2 years ago by
Ya
▴ 300
51
votes
19
replies
41k
views
6 follow
Tutorial:
Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization
bigwig
chip-seq
rna-seq
updated 5 weeks ago by
Ram
38k • written 11.0 years ago by
Sukhi Singh
11k
50
votes
3
replies
4.0k
views
Tutorial:
[[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 17 days ago by
Ram
38k • written 4.2 years ago by
ATpoint
71k
48
votes
7
replies
11k
views
7 follow
Tutorial:
Genome Assembly Review Papers
assembly
papers
updated 5 weeks ago by
Ram
38k • written 10.6 years ago by
Istvan Albert
97k
47
votes
19
replies
12k
views
8 follow
Tutorial:
Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control
fastqc
updated 11 weeks ago by
Ram
38k • written 10.1 years ago by
Istvan Albert
97k
45
votes
14
replies
59k
views
10 follow
Tutorial:
Using R in Conda
R
updated 17 days ago by
Ram
38k • written 2.7 years ago by
rohitsatyam102
▴ 690
45
votes
2
replies
35k
views
Tutorial:
Mapping Reads With Bwa And Bowtie
bowtie
bwa
updated 6 weeks ago by
Ram
38k • written 11.0 years ago by
MSU course 2011
▴ 540
44
votes
1
reply
6.2k
views
Tutorial:
Basic normalization, batch correction and visualization of RNA-seq data
edger
RNA-seq
updated 7 weeks ago by
Ram
38k • written 2.5 years ago by
ATpoint
71k
43
votes
6
replies
11k
views
Tutorial:
Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl
maf
tcga
vcf
updated 29 days ago by
Ram
38k • written 9.2 years ago by
Cyriac Kandoth
5.9k
231 results • Page
1 of 5
Recent Votes
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
Talk from Aaron Lun on Orchestrating Single-Cell Analysis With Bioconductor
SSPACE for scaffolding
Answer: Snakemake workflow for trimmomatic
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
A: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
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Popular Question
to
zhou_1228
• 0
Teacher
to
GenoMax
127k
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to
Mensur Dlakic
★ 23k
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Pierre Lindenbaum
153k
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lessismore
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onca
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Recent Replies
Comment: TCGA-BRCA tissue and RNAseq problem
by
pinheirofabiano
▴ 10
Go to https://portal.gdc.cancer.gov > Exploration > select TCGA and the cancer type you want > select case ID to download the files and hav…
Answer: Snakemake workflow for trimmomatic
by
antoine.fauchois92
• 0
Thank you very much for your reply ! It's working now !
Comment: Dependent p values
by
Eliza
▴ 20
@lchart I'm sorry for asking another of questions but I'm new to this field , can you please explain a little more how to use SKAT , saige…
Comment: How to deal with the probe id mapping to multiple gene ids?
by
dare_devil
★ 1.7k
similar question [here][1], [here][2] and [here][3] [1]: https://support.bioconductor.org/p/54838/ [2]: https://support.bioconductor.…
Comment: How to deal with the probe id mapping to multiple gene ids?
by
dare_devil
★ 1.7k
@genomax I have used the same platform file only. If you look at probe id and their corresponding `Gene Symbol` or `ENTREZ_GENE_ID` you can…
Comment: How to deal with the probe id mapping to multiple gene ids?
by
GenoMax
127k
Where are you seeing this? [Platform file for this array][1] on GEO has these names uniquely assigned. [1]: https://www.ncbi.nlm.nih.go…
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
by
rpolicastro
11k
`Org.Mm.eg.db` is the mouse organism database, but your ENSEMBL IDs are for human genes. Mouse ensembl ids start with `ENSMUSG`. You proba…
Comment: Snakemake doesn't recognize output files even though they are created
by
DdogBoss
• 0
Yes, it completed the dry run. What other information do you need?
Comment: LDSC correlation calculate confidence intervals
by
YL
▴ 10
Based on my personal thought, I think the se from LDSC output probably needs to be transferred using Delta method based on Fisher transform…
Comment: LDSC correlation calculate confidence intervals
by
YL
▴ 10
Hi, Are you able to find an answer for this? I have the exact question! YL
Answer: Gene duplicate
by
ATpoint
71k
Use use ensembID_geneName as gene identifier to avoid that. These duplicate names exist as genes so removing them is somewhat not really da…
Comment: Gene duplicate
by
Ram
38k
> some Ensembl IDs that are the same Please show us some examples.
Comment: R package for functional enrichment and depletion analysis
by
rpolicastro
11k
What you're describing is a simulation of the hypergeometric test, so if you want an exact solution you could use the function `fora` from …
Comment: How to remove duplicate reads after ONT basecalling from fastq.gz files
by
Darrenjdd
• 0
Perfect! Thank you!
Comment: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
by
Daniel
• 0
Hi, I am wondering if you ever got an answer for this question. Also, I am curious why it is true that "All the reads coming from one end…
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