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323 results • Page
1 of 7
Sort: Views
Rank
Views
Votes
Replies
282
votes
39
replies
174k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 6 months ago by
Ram
40k • written 9.1 years ago by
Obi Griffith
20k
288
votes
33
replies
99k
views
25 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 7 months ago by
Ram
40k • written 9.9 years ago by
Obi Griffith
20k
238
votes
176
replies
88k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 4 months ago by
Ram
40k • written 8.2 years ago by
TriS
★ 4.7k
86
votes
22
replies
80k
views
14 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 11 weeks ago by
sifa.khan
• 0 • written 5.2 years ago by
otwtgin2010
▴ 580
50
votes
14
replies
75k
views
10 follow
Tutorial:
Using R in Conda
R
updated 6 months ago by
Ram
40k • written 3.2 years ago by
rohitsatyam102
▴ 750
27
votes
10
replies
70k
views
9 follow
Tutorial:
Installing an updated R version (>=4.0) using conda
software-error
R
updated 6 months ago by
Ram
40k • written 2.5 years ago by
Nitin Narwade
★ 1.4k
196
votes
44
replies
70k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 8 months ago by
Ram
40k • written 11.0 years ago by
Obi Griffith
20k
75
votes
13
replies
66k
views
10 follow
Tutorial:
Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r
cancer
classification
updated 11 months ago by
Ram
40k • written 9.9 years ago by
Nicholas Spies
★ 1.2k
149
votes
35
replies
60k
views
33 follow
Tutorial:
Tools For Metagenomic Data Analysis
metagenomics
next-gen
updated 7 months ago by
Ram
40k • written 10.8 years ago by
vijay
★ 1.6k
85
votes
2
replies
56k
views
6 follow
Tutorial:
How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 7 months ago by
Ram
40k • written 10.3 years ago by
Eric Normandeau
11k
146
votes
34
replies
53k
views
17 follow
Tutorial:
Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music
cancer
tcga
mutation
maf
updated 7 months ago by
Ram
40k • written 10.5 years ago by
Cyriac Kandoth
6.0k
0
votes
3
replies
50k
views
Tutorial:
Installation VMD on LINUX_64
gromacs
VMD
updated 5 months ago by
Ram
40k • written 7.3 years ago by
Hassan Rasouli
▴ 10
65
votes
9
replies
48k
views
7 follow
Tutorial:
Reference Assembly - Mapping Reads To A Reference Genome
reference
samtools
mapping
bwa
updated 7 months ago by
Ram
40k • written 10.3 years ago by
Joseph Hughes
★ 3.0k
146
votes
70
replies
46k
views
20 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 4 weeks ago by
Raheleh
▴ 260 • written 5.9 years ago by
Kevin Blighe
86k
116
votes
66
replies
43k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
fastq-dump
Fastq
ENA
updated 6 months ago by
Ram
40k • written 5.2 years ago by
ATpoint
77k
53
votes
19
replies
42k
views
6 follow
Tutorial:
Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization
bigwig
chip-seq
rna-seq
updated 7 months ago by
Ram
40k • written 11.5 years ago by
Sukhi Singh
11k
60
votes
52
replies
41k
views
23 follow
Tutorial:
Creating Interactive Volcano Plots with R and Plot.ly
plotly
R
volcano-plot
updated 6 months ago by
Ram
40k • written 7.0 years ago by
steve
★ 3.3k
93
votes
105
replies
39k
views
25 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 6 months ago by
Ram
40k • written 5.1 years ago by
Kevin Blighe
86k
58
votes
25
replies
38k
views
15 follow
Tutorial:
Protocol To Downlad TCGA Data From GDC
GDC
methylation
TCGA
updated 6 months ago by
Ram
40k • written 7.2 years ago by
Shicheng Guo
★ 9.3k
45
votes
2
replies
36k
views
Tutorial:
Mapping Reads With Bwa And Bowtie
bowtie
bwa
updated 7 months ago by
Ram
40k • written 11.5 years ago by
MSU course 2011
▴ 540
132
votes
123
replies
33k
views
23 follow
Tutorial:
Survival analysis with gene expression
cox
gene-expression
survival-analysis
geo
updated 6 months ago by
1769mkc
★ 1.1k • written 4.9 years ago by
Kevin Blighe
86k
95
votes
25
replies
32k
views
11 follow
Tutorial:
Fastq Quality Control Shootout
quality
qc
trimming
fastq
updated 7 months ago by
Ram
40k • written 11.0 years ago by
Istvan Albert
98k
99
votes
16
replies
32k
views
18 follow
Tutorial:
Heatmaps in R
heatmap
R
updated 6 months ago by
Ram
40k • written 7.2 years ago by
Jean-Karim Heriche
26k
90
votes
19
replies
31k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray
bioconductor
expression
classification
updated 7 months ago by
Ram
40k • written 9.9 years ago by
Obi Griffith
20k
84
votes
47
replies
30k
views
28 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 1 day ago by
Ram
40k • written 10.0 years ago by
Irsan
★ 7.7k
33
votes
9
replies
30k
views
11 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 6 months ago by
Ram
40k • written 3.1 years ago by
lavinia.gordon
▴ 160
84
votes
29
replies
30k
views
20 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 9 weeks ago by
amziepickles
• 0 • written 7.6 years ago by
Obi Griffith
20k
31
votes
12
replies
28k
views
7 follow
Tutorial:
So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control
fastqc
updated 7 months ago by
Ram
40k • written 10.0 years ago by
Istvan Albert
98k
99
votes
8
replies
28k
views
8 follow
Tutorial:
Guide to TCGA data
cancer
RNA-Seq
clinical
TCGA
updated 5 months ago by
Ram
40k • written 7.6 years ago by
Jordan Anaya
★ 1.1k
71
votes
26
replies
26k
views
15 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 7 months ago by
Ram
40k • written 9.6 years ago by
Istvan Albert
98k
67
votes
6
replies
25k
views
7 follow
Tutorial:
Rna-Seq Review Papers
RNA-seq
papers
updated 7 months ago by
Ram
40k • written 11.1 years ago by
Istvan Albert
98k
73
votes
60
replies
25k
views
16 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes
PLINK
PCA
VCF
updated 7 months ago by
Ram
40k • written 6.1 years ago by
Kevin Blighe
86k
104
votes
6
replies
24k
views
6 follow
Tutorial:
Creating workflows with snakemake and conda
workflow
snakemake
conda
updated 6 months ago by
Ram
40k • written 5.1 years ago by
finswimmer
16k
51
votes
3
replies
22k
views
Tutorial:
Sam File Format - Lesser Known Tips And Tricks
sam
updated 7 months ago by
Ram
40k • written 10.7 years ago by
Ya
▴ 300
10
votes
5
replies
21k
views
Tutorial:
Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 6 months ago by
Ram
40k • written 5.2 years ago by
Shicheng Guo
★ 9.3k
59
votes
43
replies
19k
views
18 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign
pacbio
arrow
smrt-limk
updated 6 months ago by
Ram
40k • written 6.0 years ago by
Rox
★ 1.4k
34
votes
15
replies
19k
views
12 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 6 months ago by
Ram
40k • written 7.0 years ago by
martinguerrerog89
▴ 310
84
votes
21
replies
19k
views
16 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 6 months ago by
Ram
40k • written 3.0 years ago by
Hamid Ghaedi
3.0k
39
votes
6
replies
18k
views
Tutorial:
Creating chromosome karyotype plot with R and ggplot2
ggplot2
R
chromosome
karyotype
updated 4 months ago by
Ram
40k • written 6.1 years ago by
steve
★ 3.3k
42
votes
2
replies
17k
views
Tutorial:
Sequencing Technology Review Papers
sequencing
papers
updated 7 months ago by
Ram
40k • written 11.1 years ago by
Istvan Albert
98k
76
votes
70
replies
17k
views
18 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
updated 6 months ago by
Ram
40k • written 5.6 years ago by
Kevin Blighe
86k
18
votes
40
replies
17k
views
16 follow
Tutorial:
Easy way to run easily orthoMCL (Copy & paste)
all-v-all
orthomcl
updated 6 months ago by
Ram
40k • written 7.3 years ago by
Esaie
▴ 170
83
votes
34
replies
17k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 4 months ago by
adelheidkratzer
• 0 • written 5.3 years ago by
egeulgen
★ 1.3k
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 7 months ago by
Ram
40k • written 10.6 years ago by
lh3
33k
35
votes
17
replies
16k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning
classification
updated 4 months ago by
GenoMax
134k • written 9.9 years ago by
Obi Griffith
20k
30
votes
14
replies
16k
views
8 follow
Tutorial:
Installation of the MuSiC suite on unsupported Linux distributions
genome-music
linux
smg
updated 7 months ago by
Ram
40k • written 10.7 years ago by
Cyriac Kandoth
6.0k
75
votes
14
replies
15k
views
15 follow
Tutorial:
List Of Bioinformatics Books
books
updated 7 months ago by
Ram
40k • written 10.4 years ago by
Medhat
9.7k
15
votes
5
replies
15k
views
Tutorial:
How to create a mutation lolliplot with GenVisR
bioconductor
graphics
R
genvisr
updated 5 months ago by
Ram
40k • written 7.3 years ago by
Obi Griffith
20k
16
votes
7
replies
14k
views
Tutorial:
Integrating VDJ sequencing data with Seurat
VDJ
Seurat
sc-RNAseq
clonotyping
updated 6 months ago by
Ram
40k • written 4.3 years ago by
atakanekiz
▴ 310
16
votes
11
replies
14k
views
7 follow
Tutorial:
retrieve full TCGA datasets from cBioportal with R
TCGA
RNA-seq
data-retrieval
cBioportal
R
updated 6 months ago by
Ram
40k • written 6.9 years ago by
TriS
★ 4.7k
323 results • Page
1 of 7
Recent Votes
A: Individual VCF files from main VCF file
Individual VCF files from main VCF file
A: Splitting vcf files to individual samples
Splitting vcf files to individual samples
Answer: Chip-Seq and correlation of bam file
Comment: Chip-Seq and correlation of bam file
BWA mem bam output name sorted
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Comment: Unmapped Reads in Kallisto
by
dsull
★ 4.7k
Sounds good! I just added a solution here.
Answer: Unmapped Reads in Kallisto
by
dsull
★ 4.7k
Running kallisto bus with the -n option will record the read numbers of the reads that have been successfully mapped in the output BUS file…
Comment: Automate the Splitting of a VCF File by Sample (bcftools)
by
cfos4698
▴ 830
Just a comment re: your bash example reading from a file. Have you tried `while` instead of 'with'? ``` while read sample; do bcftools…
Comment: Split plink files by a number of SNPs
by
Raygozak
★ 1.4k
Out of curiosity, why would someone ask how to do something if they already knew how to do it or which tools to use? Also, the OP is not a…
Comment: Comparing multiple RNASeq studies
by
Zhenyu Zhang
▴ 980
no. The best you can do is to draw conclusion using one dataset, and validate your conclusion using other datasets.
Comment: comparision of umap single cell
by
synat.keam
▴ 80
Thank, Seniors.. I figured out the issue of my integration as I did not state the ``` reduction= "harmony" ```
Comment: Issue with merging in plink and eigensoft.
by
bk11
★ 1.2k
> I merged two datasets in plink1.9. It worked, but I did get the error > "multiple positions seen for variant" and "variants have the same…
Comment: How to subset large BAM files specifically/ extract specific subsets?
by
ella
• 0
It worked now, after re-mapping with short-headed FASTA! :) Thanks a lot again for your time.
Comment: Complex multifactorial DE analysis with limma/edgeR based on rnaseq data
by
svlachavas
▴ 780
Dear LChart, thanks a million for your detailed response and explanations !! Some quick updated comments (hopefully not disturb you furth…
Comment: Clustering in single cell
by
Chris
▴ 200
Just because the articles and tutorials I read, they usually clearly separate which I worry I did something wrong.
Comment: How to subset large BAM files specifically/ extract specific subsets?
by
GenoMax
134k
> do you think the one or other option (using fasta with shortened > headers vs. bbmap.sh with trd=t option) would have other advantages or…
Comment: Clustering in single cell
by
bk11
★ 1.2k
> However, in my analysis, clusters of each cell types are not clearly > separate even though I tried different clustering algorithms (louv…
Comment: How to subset large BAM files specifically/ extract specific subsets?
by
ella
• 0
I think I even used `reformat.sh` earlier today, but don´t remember with what arguments. I now tried what you suggested, but got an error: …
Comment: Clustering in single cell
by
Jean-Karim Heriche
26k
Are you doing the clustering in UMAP space? If so, avoid distance-based clustering because distances are only meaningful locally, i.e dista…
Comment: Github access with token headache
by
Ram
40k
Yes please.
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