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357 results • Page
1 of 8
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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
Ram
39k • written 7.8 years ago by
TriS
★ 4.6k
130
votes
123
replies
30k
views
23 follow
Tutorial:
Survival analysis with gene expression
cox
gene-expression
survival-analysis
geo
updated 10 weeks ago by
1769mkc
★ 1.1k • written 4.6 years ago by
Kevin Blighe
85k
92
votes
105
replies
36k
views
25 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 11 weeks ago by
Ram
39k • written 4.8 years ago by
Kevin Blighe
85k
76
votes
70
replies
16k
views
18 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
updated 11 weeks ago by
Ram
39k • written 5.3 years ago by
Kevin Blighe
85k
146
votes
69
replies
44k
views
19 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 9 weeks ago by
k001
▴ 10 • written 5.5 years ago by
Kevin Blighe
85k
116
votes
66
replies
41k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
fastq-dump
Fastq
ENA
updated 11 weeks ago by
Ram
39k • written 4.9 years ago by
ATpoint
72k
72
votes
60
replies
24k
views
16 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes
PLINK
PCA
VCF
updated 3 months ago by
Ram
39k • written 5.7 years ago by
Kevin Blighe
85k
60
votes
52
replies
40k
views
23 follow
Tutorial:
Creating Interactive Volcano Plots with R and Plot.ly
plotly
R
volcano-plot
updated 11 weeks ago by
Ram
39k • written 6.7 years ago by
steve
★ 3.3k
72
votes
48
replies
16k
views
15 follow
Tutorial:
For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs
alignment
bwa
updated 3 months ago by
Ram
39k • written 10.3 years ago by
lh3
33k
196
votes
44
replies
69k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 4 months ago by
Ram
39k • written 10.7 years ago by
Obi Griffith
20k
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 11 weeks ago by
Ram
39k • written 5.7 years ago by
Rox
★ 1.4k
78
votes
42
replies
29k
views
25 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 28 days ago by
Ram
39k • written 9.6 years ago by
Irsan
★ 7.7k
18
votes
40
replies
16k
views
16 follow
Tutorial:
Easy way to run easily orthoMCL (Copy & paste)
all-v-all
orthomcl
updated 11 weeks ago by
Ram
39k • written 6.9 years ago by
Esaie
▴ 170
277
votes
39
replies
168k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 10 weeks ago by
Ram
39k • written 8.8 years ago by
Obi Griffith
20k
148
votes
35
replies
59k
views
33 follow
Tutorial:
Tools For Metagenomic Data Analysis
metagenomics
next-gen
updated 3 months ago by
Ram
39k • written 10.5 years ago by
vijay
★ 1.6k
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
adelheidkratzer
• 0 • written 5.0 years ago by
egeulgen
★ 1.3k
145
votes
34
replies
52k
views
17 follow
Tutorial:
Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music
cancer
tcga
mutation
maf
updated 3 months ago by
Ram
39k • written 10.1 years ago by
Cyriac Kandoth
5.9k
277
votes
33
replies
94k
views
25 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 3 months ago by
Ram
39k • written 9.6 years ago by
Obi Griffith
20k
12
votes
31
replies
5.1k
views
6 follow
Tutorial:
gene set filter/selection for training ab initio annotation tools
geneset
genome
gene
abinitio
updated 12 weeks ago by
Ram
39k • written 3.8 years ago by
Juke34
7.9k
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
18 days ago by
Ram
39k
82
votes
28
replies
28k
views
19 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 3 months ago by
Ram
39k • written 7.2 years ago by
Obi Griffith
20k
65
votes
26
replies
11k
views
11 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 11 weeks ago by
Ram
39k • written 4.2 years ago by
finswimmer
16k
70
votes
26
replies
25k
views
15 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 3 months ago by
Ram
39k • written 9.3 years ago by
Istvan Albert
98k
64
votes
26
replies
12k
views
7 follow
Tutorial:
Parallel processing in R
biocparallel
mclapply
foreach
R
updated 11 weeks ago by
Ram
39k • written 5.7 years ago by
Kevin Blighe
85k
136
votes
25
replies
77k
views
14 follow
Tutorial:
Piping With Samtools, Bwa And Bedtools
unix
samtools
bwa
bedtools
updated 14 months ago by
Ram
39k • written 11.1 years ago by
Ying W
★ 4.2k
58
votes
25
replies
37k
views
15 follow
Tutorial:
Protocol To Downlad TCGA Data From GDC
GDC
methylation
TCGA
updated 11 weeks ago by
Ram
39k • written 6.9 years ago by
Shicheng Guo
★ 9.3k
94
votes
25
replies
31k
views
11 follow
Tutorial:
Fastq Quality Control Shootout
quality
qc
trimming
fastq
updated 3 months ago by
Ram
39k • written 10.7 years ago by
Istvan Albert
98k
9
votes
23
replies
8.6k
views
7 follow
Tutorial:
OrthoMCL installation on Ubuntu Linux
ubuntu
orthomcl
mysql
linux
updated 17 days ago by
Ram
39k • written 5.4 years ago by
vimalkvn
▴ 310
18
votes
22
replies
7.5k
views
10 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 11 weeks ago by
Ram
39k • written 3.5 years ago by
Juke34
7.9k
142
votes
21
replies
29k
views
12 follow
Tutorial:
A few words for R beginners
Swirl
R
updated 13 months ago by
Ram
39k • written 8.5 years ago by
Parham
★ 1.6k
83
votes
21
replies
16k
views
16 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 12 weeks ago by
Ram
39k • written 2.6 years ago by
Hamid Ghaedi
2.9k
82
votes
21
replies
74k
views
13 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 3 months ago by
cmdcolin
★ 3.0k • written 4.9 years ago by
otwtgin2010
▴ 540
12
votes
20
replies
12k
views
10 follow
Tutorial:
Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell
RNA-Seq
seurat
TCR
updated 11 weeks ago by
Ram
39k • written 4.0 years ago by
jared.andrews07
★ 14k
8
votes
19
replies
12k
views
9 follow
Tutorial:
A:orthomcl with local mysql server on linux server, complete install
mysql
orthomcl
updated 12 weeks ago by
Ram
39k • written 8.5 years ago by
Lesley Sitter
▴ 580
89
votes
19
replies
31k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray
bioconductor
expression
classification
updated 3 months ago by
Ram
39k • written 9.6 years ago by
Obi Griffith
20k
51
votes
19
replies
42k
views
6 follow
Tutorial:
Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization
bigwig
chip-seq
rna-seq
updated 3 months ago by
Ram
39k • written 11.1 years ago by
Sukhi Singh
11k
42
votes
19
replies
7.2k
views
8 follow
Tutorial:
Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 3 months ago by
Ram
39k • written 10.3 years ago by
Daniel Standage
4.1k
23
votes
19
replies
5.8k
views
10 follow
Tutorial:
MutScan: Detect important mutations by scanning FastQ files directly
fastq
mutation
cancer
target
updated 8 weeks ago by
Ram
39k • written 6.7 years ago by
chen
★ 2.4k
47
votes
19
replies
12k
views
8 follow
Tutorial:
Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control
fastqc
updated 4 months ago by
Ram
39k • written 10.3 years ago by
Istvan Albert
98k
12
votes
17
replies
2.3k
views
Tutorial:
How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola
bwa
updated 5 months ago by
Ram
39k • written 8.0 years ago by
Istvan Albert
98k
8
votes
17
replies
2.4k
views
Tutorial:
Simple approach to RNA-seq (T-Bioinfo platform)
alignment
next-gen-sequencing
RNA-seq
updated 9 months ago by
Ram
39k • written 7.6 years ago by
elia.brodsky
▴ 340
34
votes
17
replies
15k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning
classification
updated 4 weeks ago by
GenoMax
129k • written 9.5 years ago by
Obi Griffith
20k
26
votes
17
replies
6.8k
views
8 follow
Tutorial:
virtualenv - running Python based software in isolation
python
virtualenv
updated 8 months ago by
Ram
39k • written 8.8 years ago by
Ian
5.9k
99
votes
16
replies
30k
views
18 follow
Tutorial:
Heatmaps in R
heatmap
R
updated 11 weeks ago by
Ram
39k • written 6.8 years ago by
Jean-Karim Heriche
26k
42
votes
16
replies
21k
views
15 follow
Tutorial:
Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC
varscan2
CNV
copy-number
updated 10 months ago by
Ram
39k • written 7.7 years ago by
Chirag Nepal
★ 2.3k
24
votes
15
replies
8.1k
views
8 follow
Tutorial:
Syllabus To Learn Bioinformatics From Online Video Resources
course
training
mooc
updated 3 months ago by
Ram
39k • written 10.4 years ago by
Medhat
9.6k
34
votes
15
replies
5.3k
views
6 follow
Tutorial:
How to do data cleaning for VCF genetic file
vcf
updated 11 weeks ago by
Ram
39k • written 4.0 years ago by
Shicheng Guo
★ 9.3k
59
votes
15
replies
12k
views
Tutorial:
Which human reference genome should I use?
assembly
genome
alignment
updated 11 days ago by
Ram
39k • written 4.7 years ago by
finswimmer
16k
34
votes
15
replies
18k
views
12 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 11 weeks ago by
Ram
39k • written 6.7 years ago by
martinguerrerog89
▴ 310
30
votes
14
replies
15k
views
8 follow
Tutorial:
Installation of the MuSiC suite on unsupported Linux distributions
genome-music
linux
smg
updated 3 months ago by
Ram
39k • written 10.3 years ago by
Cyriac Kandoth
5.9k
357 results • Page
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Recent Votes
Answer: Perl script running slow with big files
C: Bedtools problem : It looks as though you have less than 3 columns at line: 1.
A: Forward And Reverse Strand Conventions
Comment: hisat2 Error 137
Comment: NCBI API, Perl
Comment: Is hg38 on the multiz 30-way alignment inaccurate?
Answer: Is it possible to add a dendrogram as a top annotation using ComplexHeatmap ?
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★ 1.5k
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Recent Replies
Comment: Is hg38 on the multiz 30-way alignment inaccurate?
by
Maximilian Haeussler
★ 1.5k
Can you provide an example? Which MAF file are you referring to, on the UCSC and Ensembl side. I can imagine a dozen different things that …
Comment: Trying to edit VCF file
by
Pierre Lindenbaum
154k
are they present in Fall22C.txt ?
Comment: Trying to edit VCF file
by
peavy
• 0
Y Z and AA ideally wont be there or come up in the vcf file if I removed them proper so I'm wondering what the issue is in the initial code.
Comment: Trying to edit VCF file
by
Pierre Lindenbaum
154k
> I noticed that there was still columns for what I removed from the file. so, what should we see in your image ??
Comment: Trying to edit VCF file
by
peavy
• 0
![The last 3 columns are what I thhought I deleted ][1] [1]: /media/images/709ceea6-da38-47e3-b4ab-13727837
Comment: NCBI API, Perl
by
GenoMax
129k
Using EntrezDirect: $ esearch -db nuccore -query LOC105370256 | efetch -format acc | grep -v NC | xargs -n 1 sh -c 'efetch -db nuccore…
Comment: calculate p value and associated z score for snp-gene pair
by
LChart
2.6k
I think researchers would agree that FDR > 0.05 is not significant, though some would argue FDR between 0.05 and 0.1 is OK for an initial f…
Comment: Trying to edit VCF file
by
Pierre Lindenbaum
154k
> When I opened the vcf in excel I noticed that there was still columns for what I removed from the file. please, explain, show the data.…
Comment: hisat2 Error 137
by
Forough
▴ 10
Thank you very much for sending the like. I will try it.
Comment: Which method is the best for using in "dba.count" in Diffbind R package
by
Jo
• 0
Thank you for all the helpful advice and explanations. Can you further explain this part: > "The default normalization factors (based sol…
Comment: VEP tab/vcf - Different output
by
Ram
39k
I don't think so, no. EnsEMBL seems to have come up with a verbose explanation for why they don't want to put in the effort.
Comment: VEP tab/vcf - Different output
by
Jeremy Leipzig
21k
is there any way to report the VCF-style ref and alt in the VEP tabular output?
Comment: Is hg38 on the multiz 30-way alignment inaccurate?
by
Daniel
▴ 30
Thank you! If I understand correctly, it's possible that the coordinates/sequences may not be the same anymore, because the maf files use t…
Comment: NCBI API, Perl
by
alessandro.alma00
• 0
Sorry i didn't want to be rude.. Thank you for helping me, im sorry but its the first time I use API tbh... i will like to retrieve the seq…
Comment: How to perform statistical analysis of label free experiment using results from
by
Ram
39k
Do not add answers unless you're actually answering the question. Use `Add Comment` instead. I've moved your post this time, be careful in …
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