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1,000 results • Page
1 of 20
Sort: Views
Rank
Views
Votes
Replies
23
votes
22
replies
45k
views
6 follow
Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking …
plink
vcf
fam
gatk
vcftools
updated 12 months ago by
Nicole
• 0 • written 5.6 years ago by
gaelgarcia
▴ 250
4
votes
4
replies
38k
views
How to convert a URL into a DOI programmatically
pubmed
doi
url
written 7.2 years ago by
entheologist33
▴ 100
4
votes
13
replies
31k
views
6 follow
[main_samview] fail to read the header from sample.bam
alignment
updated 17 months ago by
Qboy
• 0 • written 5.7 years ago by
sambioinfo2018
▴ 20
20
votes
15
replies
28k
views
8 follow
Converting SNP from chr:pos to rs number using PLINK?
plink
SNP
updated 16 months ago by
Ram
41k • written 7.9 years ago by
dam4l
▴ 200
2
votes
3
replies
27k
views
How to extract vcf.gz and vcf.gz.tbi
SNP
sequence
gene
updated 5.4 years ago by
Pierre Lindenbaum
158k • written 5.4 years ago by
elhlalisoufiane
▴ 30
5
votes
6
replies
27k
views
terminate called after throwing an instance of 'std::bad_alloc?
bedtools
linux
data
4.6 years ago by
star
▴ 350
3
votes
4
replies
22k
views
Using nr database for BLAST search
nr
database
blast
blastp
updated 7.2 years ago by
Biostar
20 • written 7.4 years ago by
cookm346
▴ 20
9
votes
4
replies
22k
views
What is the definition of "read depth" vs "coverage"? (again...)
coverage
depth
read depth
6.6 years ago by
ariel.balter
▴ 220
2
votes
4
replies
21k
views
Error in file(file, "rt") : cannot open the connection
R
MicroRNA TXT FORMAT
updated 7.6 years ago by
GenoMax
136k • written 7.6 years ago by
31sharmajittu1991
• 0
27
votes
17
replies
20k
views
12 follow
Dotplot for filtered pathways result
pathways
ggplot2
clusterProfiler
r
dotplot
24 months ago by
Leite
★ 1.3k
7
votes
16
replies
19k
views
featureCounts: Low percentage of assigned fragments
RNA-Seq
rna-seq
7.3 years ago by
aggregatibacter
▴ 180
3
votes
3
replies
19k
views
Subsetting - Raw Counts from Seurat Object
seurat
raw counts
RNA-Seq
3.6 years ago by
David_emir
▴ 470
1
vote
5
replies
19k
views
Calculating the sequence similarity and percentage of matched sequences
alignment
sequence
updated 6.0 years ago by
eteleeb
• 0 • written 6.1 years ago by
ago1mutant
▴ 10
2
votes
8
replies
17k
views
Using vcfutils.pl command
alignment
updated 19 months ago by
Ram
41k • written 8.8 years ago by
lcc1844
▴ 40
2
votes
10
replies
17k
views
How do you use the Aspera ascp command?
aspera
gigascience
gigaDb
updated 2.2 years ago by
Ram
41k • written 8.1 years ago by
cyril-cros
▴ 940
16
votes
38
replies
16k
views
Differential gene Analysis by Limma
Limma
Microarray
R
updated 19 months ago by
Ram
41k • written 8.8 years ago by
Mo
▴ 920
2
votes
13
replies
16k
views
convert text file to fasta file
blast
updated 7.3 years ago by
GouthamAtla
12k • written 7.3 years ago by
sukesh1411
▴ 30
16
votes
14
replies
16k
views
Which truseq trimmomatic adapters file to use when removing truseq adapters?
adapters
trimmomatic
RNA-seq
5.4 years ago by
salamandra
▴ 550
0
votes
8
replies
16k
views
find ORF in sequence python
sequence
updated 6.9 years ago by
natasha.sernova
★ 3.9k • written 6.9 years ago by
elisheva
▴ 120
6
votes
2
replies
16k
views
Pacbio Ccs Vs Subreads Explained ?
updated 9.6 years ago by
Biostar
20 • written 10.1 years ago by
curious.genome
▴ 40
5
votes
4
replies
16k
views
glmnet package lasso error
glmnet
lasso
multilinear regression
5.7 years ago by
demoraesdiogo2017
▴ 100
13
votes
13
replies
16k
views
How to interpret Per sequence GC content module in FastQC for RNA-seq data?
RNA-Seq
FastQC
QC
GC-content
4.3 years ago by
Arindam Ghosh
▴ 510
0
votes
3
replies
15k
views
How to choose a TPM cut-off point
RNA-Seq
transcript
tpm
updated 15 months ago by
Ram
41k • written 8.1 years ago by
amyfm
▴ 10
2
votes
2
replies
15k
views
How to calculate the insert size for Paired-end reads
SSPACE
insert-size
7.4 years ago by
Ric
▴ 430
4
votes
10
replies
15k
views
How to plot a multiple line graph with Mean and Std Error for following dataset?
R
updated 5.6 years ago by
GenoMax
136k • written 5.6 years ago by
WUSCHEL
▴ 720
1
vote
5
replies
15k
views
pheatmap: how to use legend information as row annotation?
R
pheatmap
legend
annotation
5.6 years ago by
n85825
• 0
2
votes
4
replies
15k
views
TRIMMOMATRIC Nextera trimming
next-gen
updated 13 months ago by
Ram
41k • written 8.3 years ago by
meekadi
▴ 10
4
votes
18
replies
15k
views
Alignment with BWA and SAMtools
BWA
SAM-file
SAMtools
updated 3.1 years ago by
Biostar
20 • written 5.3 years ago by
Shelle
▴ 30
3
votes
8
replies
15k
views
Error when running pheatmap
pheatmap
Error in hclust
4.7 years ago by
luzglongoria
▴ 50
1
vote
8
replies
15k
views
How to update rlang in R?
rlang
R
14 months ago by
Amr
▴ 140
8
votes
4
replies
14k
views
Use of if-else statement in snakemake rule
snakemake
if-else
python
updated 4.0 years ago by
schroder.julia
• 0 • written 6.4 years ago by
Jokhe
▴ 140
1
vote
8
replies
14k
views
HTSeq-count high number of no_feature
htseq-count
rna-seq
updated 19 months ago by
Ram
41k • written 8.8 years ago by
cafelumiere12
▴ 80
3
votes
1
reply
14k
views
How do you normalize Transcript per Million TPM to compare between samples ?
RNA-Seq
TPM
STAR
salmon
quantification
6.9 years ago by
ZheFrench
▴ 540
0
votes
3
replies
14k
views
Error in (function (classes, fdef, mtable): unable to find an inherited method for function ‘annotation’ for signature ‘"character
inSilicoMerging
9.5 years ago by
ira_grich
• 0
9
votes
13
replies
14k
views
Sort bam file by coordinates using samtools
next-gen-sequencing
gene
rna-seq
updated 5 months ago by
Ram
41k • written 5.2 years ago by
Shahzad
▴ 30
9
votes
13
replies
14k
views
GC Content of Fasta file --- Python Help
sequence
6.8 years ago by
Patrick Brennan
▴ 50
6
votes
13
replies
14k
views
Fastq file is truncated error message
RNA-Seq
error
fastq
7.5 years ago by
rob.costa1234
▴ 310
4
votes
1
reply
14k
views
Converting BigBed to Bed format
Installing BigFile Support
8.5 years ago by
sumaira.zaman10
▴ 20
0
votes
3
replies
14k
views
How to change/remove name of annotation ComplexHeatmap package?
ComplexHeatmap
R
RNA-Seq
annotations
updated 3.5 years ago by
Ram
41k • written 3.5 years ago by
camillab.
▴ 150
0
votes
2
replies
13k
views
Error in -delete: invalid argument to unary operator
RNA-Seq
R
3.8 years ago by
ovariohisterectomia
▴ 40
8
votes
5
replies
13k
views
The comparison between HISAT2 and Tophat2
RNA-Seq
Tophat2
HISAT2
updated 5.2 years ago by
Ram
41k • written 7.8 years ago by
Peng Huang
▴ 50
6
votes
13
replies
13k
views
Showing FDR and log2FC in Volcano plot using R
R
RNA-Seq
volcano plot
updated 4.5 years ago by
zx8754
11k • written 6.0 years ago by
Farbod
★ 3.4k
0
votes
2
replies
13k
views
How to download pfam database
sequence
updated 6.9 years ago by
Medhat
9.7k • written 6.9 years ago by
Sanchita Gupta
▴ 30
3
votes
11
replies
13k
views
What is the acceptable % of reads that map to no feature (in RNASeq)?
htseq
RNA-Seq
STAR
updated 19 months ago by
Ram
41k • written 8.9 years ago by
noushin.farnoud
▴ 120
1
vote
13
replies
13k
views
"[E::bgzf_read] Read block operation failed" error - possible truncation/corruption of BAM file
samtools
updated 2.5 years ago by
darklings
▴ 560 • written 4.1 years ago by
gordo2b
• 0
0
votes
4
replies
13k
views
Unable to install XLconnect package in R studio version 3.2.1
R
updated 14 months ago by
Ram
41k • written 8.3 years ago by
Debbie
▴ 10
2
votes
1
reply
13k
views
Rename Idents in Seurat Object
RNA-Seq
3.5 years ago by
Thorerges
▴ 10
1
vote
2
replies
13k
views
kart file in prefetch
rna-seq
updated 7.1 years ago by
Biostar
20 • written 7.3 years ago by
zh.khodadadi
▴ 20
4
votes
12
replies
12k
views
STAR alignment error- Segmentation fault (core dumped)
alignment
software error
RNA-Seq
STAR
5.4 years ago by
EagleEye
7.5k
0
votes
2
replies
12k
views
GSEA error - After pruning, none of the gene sets passed size thresholds
RNA-Seq
GSEA
gene
genome
updated 4.3 years ago by
Morris_Chair
▴ 340 • written 4.3 years ago by
limjustinj
• 0
1,000 results • Page
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Recent Votes
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You're right. I would get help from StackExchange sites and GPT
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Thanks for the answe and the linkI used bioinfokit tpm formula to calculate tpm from bulk which is the same formula given in your link: …
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Thanks Brian for the suggestion. However, I did the whole process, from bulk counts generation, to data transformation and scrna deconvolut…
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