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Showing :
questions
6
votes
6
replies
4.8k
views
10x to cloupe
single-cell-transcriptomics
10x
6 months ago by
firestar
★ 1.6k
1
vote
0
replies
617
views
Which zUMIs output to use for differential gene expression?
zumis
rnaseq
smartseq3
single-cell
14 months ago by
firestar
★ 1.6k
3
votes
6
replies
6.2k
views
h5ad cellxgene to R
single-cell
h5
cellxgene
anndata
R
15 months ago by
firestar
★ 1.6k
3
votes
5
replies
961
views
fastq_screen error: Failed to calculate read length
fastq_screen
18 months ago by
firestar
★ 1.6k
0
votes
0
replies
722
views
Seurat analysis without ribosomal genes
single-cell
transcriptomics
seurat
18 months ago by
firestar
★ 1.6k
3
votes
2
replies
1.3k
views
Tools/pipeline for analysis of smart-seq3 data
single-cell
transcriptomics
20 months ago by
firestar
★ 1.6k
2
votes
3
replies
997
views
Differential transcript expression / differential isoform expression tool tutorial
RNA-seq
updated 21 months ago by
Ram
44k • written 21 months ago by
firestar
★ 1.6k
5
votes
4
replies
1.4k
views
Running nf-core rnaseq with smart-seq3 data
smart-seq3
nf-core
nextflow
22 months ago by
firestar
★ 1.6k
3
votes
7
replies
5.0k
views
6 follow
Cellranger count pipestance failed: The read lengths are incompatible with all the chemistries
10x
cellranger
single-cell
updated 22 months ago by
GenoMax
146k • written 2.3 years ago by
firestar
★ 1.6k
4
votes
5
replies
1.3k
views
6 follow
Exon counts do not match gene and transcript counts
salmon
rnaseq
nf-core
featurecounts
exon
updated 23 months ago by
jared.andrews07
★ 17k • written 24 months ago by
firestar
★ 1.6k
3
votes
12
replies
3.5k
views
CellRanger runs into error when running fastq files from SRA
cellranger
10x
single-cell
sra
2.1 years ago by
firestar
★ 1.6k
1
vote
3
replies
1.5k
views
Find clusters using marker genes
seurat
single-cell
cell-typing
sc-rnaseq
2.2 years ago by
firestar
★ 1.6k
2
votes
3
replies
1.4k
views
Cell ranger reads do not match Seurat reads
10x
cellranger
seurat
updated 2.9 years ago by
swbarnes2
14k • written 2.9 years ago by
firestar
★ 1.6k
3
votes
6
replies
1.7k
views
Gene names to Protein (cell surface markers) mapping
cell
transcriptomics
surface
marker
proteomics
2.9 years ago by
firestar
★ 1.6k
4
votes
4
replies
3.5k
views
Bad volcano plot
diferential-gene-expression
rna-seq
sc-rnaseq
updated 3.1 years ago by
m.sadman.sakib
▴ 120 • written 3.1 years ago by
firestar
★ 1.6k
4
votes
12
replies
2.8k
views
TMM normalized TPM
RNA-Seq
3.6 years ago by
firestar
★ 1.6k
2
votes
2
replies
7.3k
views
Seurat: Assay to use for differential expression in an integrated data
seurat
10x
single-cell
RNA-Seq
3.6 years ago by
firestar
★ 1.6k
0
votes
2
replies
3.4k
views
Merging integrated datasets
single-cell RNA-Seq
Seurat
R
integration
3.7 years ago by
firestar
★ 1.6k
48
votes
15
replies
17k
views
10 follow
DESeq2 compare all levels
differential-gene-expression
RNA-Seq
DESeq2
updated 6 months ago by
Bionaught
• 0 • written 6.3 years ago by
firestar
★ 1.6k
1
vote
2
replies
1.0k
views
Evaluate genome annotation quality
annotation
genome
updated 4.1 years ago by
hugo.avila
▴ 530 • written 4.1 years ago by
firestar
★ 1.6k
3
votes
1
reply
2.1k
views
RNA Seq: Differential expression model formula
RNA-Seq
R
DESeq
edgeR
updated 4.6 years ago by
Biostar
20 • written 8.3 years ago by
firestar
★ 1.6k
5
votes
3
replies
5.1k
views
RNA velocity plot demystified
rna-velocity
velocyto
single-cell
updated 4.7 years ago by
dchatterjee
▴ 30 • written 4.7 years ago by
firestar
★ 1.6k
0
votes
1
reply
6.4k
views
Moving data from Seurat to ScanPy
seurat
scanpy
single-cell
R
python
updated 4.7 years ago by
khorms
▴ 230 • written 4.7 years ago by
firestar
★ 1.6k
2
votes
3
replies
1.8k
views
Downstream applications of Differential transcript expression
RNA-Seq
updated 4.9 years ago by
Biostar
20 • written 7.2 years ago by
firestar
★ 1.6k
4
votes
3
replies
7.6k
views
Loading PLINK files to Haploview
plink
haploview
SNP
updated 3.0 years ago by
Nai
▴ 50 • written 6.7 years ago by
firestar
★ 1.6k
0
votes
1
reply
2.0k
views
Variant calling pacbio bacteria
pacbio
variant-calling
bacteria
sniffles
pbsv
updated 5.1 years ago by
Billy Rowell
▴ 330 • written 5.2 years ago by
firestar
★ 1.6k
1
vote
1
reply
2.2k
views
Converting bax.h5 to CCS reads
pacbio
5.2 years ago by
firestar
★ 1.6k
1
vote
3
replies
6.7k
views
Fixing batch effect with seurat integrate
scrna.seq
seurat
single-cell
5.2 years ago by
firestar
★ 1.6k
28
votes
30
replies
7.8k
views
6 follow
Similarity between two FASTA files
similarity
distance
updated 5.3 years ago by
Biostar
20 • written 6.2 years ago by
firestar
★ 1.6k
0
votes
1
reply
2.2k
views
Applications of TPM normalisation
RNA-Seq
deseq2
normalisation
dge
5.4 years ago by
firestar
★ 1.6k
0
votes
0
replies
1.4k
views
Model selection for differential expression
RNA-Seq
methylation
limma
differential expression
5.5 years ago by
firestar
★ 1.6k
7
votes
2
replies
3.5k
views
Multiple sequence alignment and visualisation for bacterial genomes
bacteria
alignment
MSA
sequencing
genome
5.6 years ago by
firestar
★ 1.6k
4
votes
5
replies
4.3k
views
Median coverage from BAM file
coverage
DNA-Seq
5.7 years ago by
firestar
★ 1.6k
4
votes
1
reply
3.2k
views
PacBio merge runs
pacbio
assembly
5.8 years ago by
firestar
★ 1.6k
1
vote
5
replies
1.2k
views
Fasta length does not match Ensembl info
annotation
fasta
updated 6.0 years ago by
Nicolas Rosewick
11k • written 6.0 years ago by
firestar
★ 1.6k
0
votes
1
reply
1.4k
views
Mauve export similarity
multiple-sequence-alignment
mauve
updated 17 months ago by
Ram
44k • written 6.2 years ago by
firestar
★ 1.6k
3
votes
1
reply
1.9k
views
Removing reads from fastq file based on position
RNA-Seq
next-gen-sequencing
updated 2.2 years ago by
Ram
44k • written 8.6 years ago by
firestar
★ 1.6k
33
votes
4
replies
42k
views
Raw counts to TPM in R
RNA-Seq
R
updated 3 months ago by
ATpoint
85k • written 6.1 years ago by
firestar
★ 1.6k
4
votes
11
replies
1.8k
views
RNA-Seq identify stably expressed genes
rna-seq
dge
6.5 years ago by
firestar
★ 1.6k
18
votes
14
replies
21k
views
bwa mem: Passing a variable to read group
bwa
bwa-mem
alignment
variant calling
gatk
6.5 years ago by
firestar
★ 1.6k
1
vote
2
replies
2.0k
views
GATK: .ped vs .fam and missing values
gatk
SNP
variant-calling
updated 6.5 years ago by
Kevin Blighe
88k • written 6.5 years ago by
firestar
★ 1.6k
3
votes
2
replies
5.5k
views
RNASeq: Differential gene expression and qqplot
limma
differential-gene-expression
RNA-Seq
deseq2
updated 6 months ago by
Ram
44k • written 6.6 years ago by
firestar
★ 1.6k
4
votes
6
replies
2.2k
views
RNA-Seq DGE: Evaluate model quality
differential-gene-expression
RNA-Seq
deseq2
updated 6 months ago by
Ram
44k • written 6.6 years ago by
firestar
★ 1.6k
12
votes
13
replies
4.9k
views
RNA-Seq DGE using PCA components as covariate
differential-gene-expression
RNA-Seq
glm
DESeq2
updated 6 months ago by
Ram
44k • written 6.6 years ago by
firestar
★ 1.6k
0
votes
4
replies
7.2k
views
Plink: compute LD between all SNP pairs
plink
SNP
linkage disequilibrium
LD
updated 6.7 years ago by
chrchang523
11k • written 6.7 years ago by
firestar
★ 1.6k
1
vote
5
replies
2.0k
views
Regenotype vcf using some samples as reference
vcf
variant-calling
SNP
6.7 years ago by
firestar
★ 1.6k
0
votes
4
replies
2.0k
views
phasing SNPs with 3 siblings
variant-calling
SNP
updated 6.7 years ago by
Pierre Lindenbaum
164k • written 6.7 years ago by
firestar
★ 1.6k
2
votes
9
replies
2.0k
views
Identifying variants differing between control/treatment
gatk
variant-calling
SNP
INDEL
updated 6.7 years ago by
Pierre Lindenbaum
164k • written 6.7 years ago by
firestar
★ 1.6k
1
vote
6
replies
2.2k
views
DGE on protein-coding and lncRNAs separately?
differential-gene-expression
RNA-seq
updated 6 months ago by
Ram
44k • written 6.9 years ago by
firestar
★ 1.6k
5
votes
8
replies
4.2k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 6 months ago by
Ram
44k • written 6.9 years ago by
firestar
★ 1.6k
63 results • Page
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