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questions
0
votes
0
replies
737
views
combine shRNA-Seq on gene level
shRNA-seq
NGS
limma
roast
5.4 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
1.2k
views
calculating extinction coefficient for thousands of peptides
extinction
extinction coefficient
peptides
cran
5.5 years ago by
Assa Yeroslaviz
★ 1.8k
47
votes
10
replies
22k
views
9 follow
The Difference Between Directional And Nondirectional Sequencing
non
sequencing
rna
updated 5.8 years ago by
julianasrinjuli
• 0 • written 12.4 years ago by
Assa Yeroslaviz
★ 1.8k
1
vote
7
replies
5.2k
views
unmapped reads in paired-end run pf bowtie2
paired-end
bowtie
unmapped-reads
updated 5.9 years ago by
Devon Ryan
104k • written 5.9 years ago by
Assa Yeroslaviz
★ 1.8k
1
vote
3
replies
2.4k
views
extracting orphan reads from bam file
bam
samtools
bwa
updated 13 months ago by
Ram
43k • written 6.0 years ago by
Assa Yeroslaviz
★ 1.8k
4
votes
9
replies
2.6k
views
detecting insertion sites of transgene in mouse genome
transgene
insertion
blast
WGS
updated 6.1 years ago by
Carambakaracho
★ 3.2k • written 6.1 years ago by
Assa Yeroslaviz
★ 1.8k
3
votes
2
replies
9.7k
views
Bed File Bedpe Format
bedtools
bam
bed
conversion
updated 6.1 years ago by
Biostar
20 • written 12.8 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
1
reply
1.7k
views
has anyone ever worked with the CNCI tool
CNCI
lncRNA
non-coding
updated 6.1 years ago by
Biostar
20 • written 6.2 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
911
views
How to analyse data from genetic screening followed by NGS ?
screening
gene-trapping
gRNA
crispr
DE-analysis
6.2 years ago by
Assa Yeroslaviz
★ 1.8k
3
votes
5
replies
4.9k
views
subset gtf file based on coordinates
RNA-Seq
bed
gtf
subset
genomic ranges
updated 6.2 years ago by
ATpoint
82k • written 6.2 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
2
replies
1.4k
views
DE analysis of lncRNA from C elegans
lncRNA
differential expression
deseq2
limma
updated 6.3 years ago by
swbarnes2
14k • written 6.3 years ago by
Assa Yeroslaviz
★ 1.8k
2
votes
4
replies
3.0k
views
allelic specific expression with Kallisto
Kallisto
ASE
allele-specific
mapping
RNA-Seq
6.3 years ago by
Assa Yeroslaviz
★ 1.8k
1
vote
2
replies
1.3k
views
Hierarchical mapping of RNA-Seq data
mapping
RNA-Seq
Hierarchical
updated 6.4 years ago by
Rob
6.5k • written 6.4 years ago by
Assa Yeroslaviz
★ 1.8k
9
votes
1
reply
13k
views
Heat Map With Two Color Scales
heatmap
r
updated 6.4 years ago by
Biostar
20 • written 10.5 years ago by
Assa Yeroslaviz
★ 1.8k
6
votes
8
replies
2.6k
views
Differential expression analysis of non-coding RNA-Seq data
deseq2
edger
ncRNA
updated 6.5 years ago by
Biostar
20 • written 6.6 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
1
reply
2.2k
views
Time series analysis from ChIP-Seq data
ChIP-Seq
time-course
time-series
updated 6.5 years ago by
GouthamAtla
12k • written 6.6 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
2
replies
1.2k
views
calling objects from an embedded function
function
nested-function
object
6.6 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
6
replies
1.8k
views
geom_line with hclust data of expression matrix
ggplot
hclust
clustering
6.6 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
1.1k
views
genome-wide gene occupancy profiles
ChIP-Seq
occupany profile
bedgraph
6.7 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
1.2k
views
ChIP-chip ANalysis of NimbleGen tiling arrays
chip-chip
peak-calling
differential-binding
arrays
6.7 years ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
2.5k
views
how to calculate with metadata of GRanges Objects
genomicranges
rtracklayer
bigwig
granges
macs2
6.7 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
2
replies
1.6k
views
How does differences in library size infuences ChIP-Seq experiments?
ChIP-Seq
library
normalisation
updated 6.9 years ago by
Istvan Albert
100k • written 6.9 years ago by
Assa Yeroslaviz
★ 1.8k
9
votes
5
replies
2.9k
views
Searching For Deletion In A Low Number Of Reads
tophat
indel
mitochondria
updated 7.0 years ago by
Biostar
20 • written 11.6 years ago by
Assa Yeroslaviz
★ 1.8k
3
votes
14
replies
2.1k
views
6 follow
Read a text file into a list
r
list
updated 7.1 years ago by
zx8754
11k • written 7.1 years ago by
Assa Yeroslaviz
★ 1.8k
8
votes
6
replies
8.1k
views
understanding multi-mapped reads
tophat2
multi-mapped
unique
samtools
updated 7.3 years ago by
Carlo Yague
8.7k • written 7.3 years ago by
Assa Yeroslaviz
★ 1.8k
1
vote
6
replies
2.2k
views
BLAT against nt
BLAT
nt
contamination
2bit
fasta
7.3 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
1
reply
1.6k
views
compare rows of colData and count Matrix
dexseq
deseq
matrix
7.3 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
1
reply
1.6k
views
retrieve organism from protein list
proteom
RNA-Seq
blast
updated 7.3 years ago by
shenwei356
8.5k • written 7.3 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
2.0k
views
why does ReportingTools does not work with yeast annotations
reportingTools
yeast
R
annotations
7.4 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
2
replies
22k
views
export list objects to XLS files
WriteXLS
xlsx
lists
updated 7.5 years ago by
ssv.bio
▴ 200 • written 7.5 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
2.7k
views
edgeR User Guide batch effect question
edgeR
batch
correlation
7.6 years ago by
Assa Yeroslaviz
★ 1.8k
2
votes
10
replies
3.1k
views
finding significance between transcripts in a RNA-Seq experiment
tximport
deseq2
edger
limma
kallisto
7.7 years ago by
Assa Yeroslaviz
★ 1.8k
2
votes
5
replies
2.0k
views
Significance within conditions
RNA-Seq
dexseq
deseq2
cuffdiff
kallisto
7.8 years ago by
Assa Yeroslaviz
★ 1.8k
4
votes
20
replies
6.1k
views
reduced quality in a paired-end R2 reads
QC
quality
fastqc
rna-seq
ChIP-Seq
updated 7.9 years ago by
Brian Bushnell
20k • written 7.9 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
1.8k
views
identification of cryptic introns splice events
cryptic introns
splice events
alternative splicing
8.0 years ago by
Assa Yeroslaviz
★ 1.8k
11
votes
5
replies
8.2k
views
following Kallisto with DESeq2 using tximport package
tximport
kallisto
deseq2
ucsc
ensembl
updated 21 months ago by
Ram
43k • written 8.3 years ago by
Assa Yeroslaviz
★ 1.8k
4
votes
5
replies
5.6k
views
HOWTO extract regions from GRanges object
GenomicRanges
R
GRanges
IRanges
updated 21 months ago by
Ram
43k • written 8.3 years ago by
Assa Yeroslaviz
★ 1.8k
4
votes
1
reply
2.9k
views
inconsistency of Mfuzz clustering
expression-profile
Mfuzz
clustering
updated 21 months ago by
Ram
43k • written 8.4 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
2
replies
2.8k
views
maSigPro warnings in glm.fit
rnaseq
glm.fit
masigpro
updated 21 months ago by
Ram
43k • written 8.4 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
7
replies
7.0k
views
fastqc Exception in thread "Thread-1" (error)
fastq
fastqc
8.5 years ago by
Assa Yeroslaviz
★ 1.8k
1
vote
2
replies
1.9k
views
HOWTO get alternative splicing event for a specific gene
UCSC
splice-variants
alternative-splicing
updated 20 months ago by
Ram
43k • written 8.5 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
1.6k
views
COMPLEAT analysis - Score calculation
enrichment
COMPLEAT
protein
updated 20 months ago by
Ram
43k • written 8.7 years ago by
Assa Yeroslaviz
★ 1.8k
2
votes
5
replies
3.5k
views
Illumina Sentrix Beads Arrays
illumina
updated 8.9 years ago by
Chris Evelo
10k • written 11.7 years ago by
Assa Yeroslaviz
★ 1.8k
2
votes
5
replies
3.3k
views
QuasiSeq vs. DESeq2 results
deseq2
normalisation
quasiseq
erccdashboard
updated 16 months ago by
Ram
43k • written 8.9 years ago by
Assa Yeroslaviz
★ 1.8k
10
votes
10
replies
3.8k
views
CLC GW vs. tophat2
tophat
CLC
fastqc
updated 16 months ago by
Ram
43k • written 8.9 years ago by
Assa Yeroslaviz
★ 1.8k
3
votes
20
replies
5.1k
views
Removing bacterial contamination of mouse gut sequences through metagenomic techniques
metagenomics
de-novo
blast
RNA-Seq
updated 15 months ago by
Ram
43k • written 9.0 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
2.8k
views
lowess normalization of FPKM
lowess
FPKM
cuffdiff
cuffdif
updated 15 months ago by
Ram
43k • written 9.0 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
2.6k
views
comparing count data with a vector of quantitative Scores
score
correlation
regression
9.0 years ago by
Assa Yeroslaviz
★ 1.8k
21
votes
9
replies
25k
views
Is There A Way To Run Fastqc On All The Fastq Files In The Different Directories With Just One Command?
fastqc
pipeline
updated 2.0 years ago by
Ram
43k • written 10.5 years ago by
Assa Yeroslaviz
★ 1.8k
2
votes
6
replies
3.3k
views
converting ensembl IDs to Entrez Ids with eutils
eutils
entrez
ensembl
conversion
biomaRt
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
Assa Yeroslaviz
★ 1.8k
200 results • Page
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